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Computational Structural Biology Methods and Applications 1st Edition Torsten Schwede
Computational Structural Biology Methods and
Applications 1st Edition Torsten Schwede Digital Instant
Download
Author(s): Torsten Schwede, Torsten Schwede, Manuel C. Peitsch
ISBN(s): 9789812778772, 9812778772
Edition: 1
File Details: PDF, 62.93 MB
Year: 2008
Language: english
Computational Structural Biology Methods and Applications 1st Edition Torsten Schwede
6659tp.indd 1 1/31/08 7:43:05 PM
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World Scientific
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Library of Congress Cataloging-in-Publication Data
Computational structural biology : methods and applications / editors, Torsten Schwede,
Manuel C. Peitsch.
p. ; cm.
Includes bibliographical references and index.
ISBN-13: 978-981-277-877-2 (hardcover : alk. paper)
ISBN-10: 981-277-877-2 (hardcover : alk. paper)
1. Proteins--Structure--Computer simulation. 2. Protein folding--Computer simulation.
3.Proteins--Structure--Mathematical models. 4. Protein folding--Mathematical models.
5. Computational biology. I. Schwede, Torsten. II. Peitsch, Manuel C.
[DNLM: 1. Computational Biology--methods. 2. Protein Conformation. 3. Drug Design.
4. Nucleic Acid Conformation. 5. Protein Folding. 6. RNA. QU 26.5 C7385 2008]
QP551.C714 2008
572'.6330285--dc22
2008001880
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A catalogue record for this book is available from the British Library.
Typeset by Stallion Press
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Printed in Singapore.
Published by
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USA office: 27 Warren Street, Suite 401-402, Hackensack, NJ 07601
UK office: 57 Shelton Street, Covent Garden, London WC2H 9HE
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Distortions
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Copyright © 2008 by World Scientific Publishing Co. Pte. Ltd.
All rights reserved. This book, or parts thereof, may not be reproduced in any form or by any means,
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1
Preface
Computational structural biology aims primarily at establishing
sequence-structure-function relationships for biological molecules
using in silico techniques. This discipline emerged about 40 years ago
(Levitt M. (2001). Nature Struct Biol 8:392–393) and has made
much progress in the past decade. The purpose of this book is to pro-
vide an overview of the progress in the field and to articulate some of
the key challenges for the coming years. By no means could we cover
the field comprehensively in just one book, and we thus focused on
the structure and function of proteins and RNAs.
The advent of large genome sequencing reinforced the observa-
tion that structural information is needed to understand the detailed
function and mechanism of biological molecules such as enzyme reac-
tions and molecular recognition events. Furthermore, structures are
obviously key to the design of molecules with new or improved func-
tions. In this context, computational structural biology emerged as a
discipline to develop computational tools to analyze and predict
molecular structures and simulate their dynamical behavior. These
theoretical approaches provide valuable insights into the detailed basis
of molecular function and enable the effective design of experimental
approaches to functional genomics. Major research topics include
protein and RNA structure prediction, protein folding, protein and
RNA dynamics with emphasis on large complexes and assemblies,
molecular recognition, drug discovery and protein engineering.
A key motivation for putting together this book came from our
own experience, as 15 years ago we established the Swiss-Model, the
first Web-based server for protein structure modeling. One major
driver behind our vision was to mask much of the complexity associ-
ated with protein modeling behind a simple interface, thereby pro-
viding the scientific community with the possibility to gain insights
v
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into the 3D structures of proteins of interest, without the need to
learn and purchase complex and expensive software. There are prob-
ably three major factors contributing to the success of the Swiss-
Model. First, the server is easy to use, as the Web-interface removes
most of the complexity normally associated with protein modeling.
Second, DeepView (also known as the Swiss-PdbViewer), which is
available for most relevant computer platforms, has many powerful
and easy-to-use features developed by modelers for modelers. Third,
the uninterrupted operations for 15 years has allowed us to develop a
robust and stable system. Today, well over 60,000 users build in
excess of 400,000 models every single year and can access over a mil-
lion pre-computed models available in the Swiss-Model Repository.
Our objective is to continuously improve the performance of the
server and the quality of the models it generates.
We are particularly thankful to Nicolas Guex for his many crucial
contributions to the development efforts of the Swiss-Model and the
DeepView and to Gale Rhodes of the University of Southern Maine
for coordinating the active DeepView user community. We also thank
Alexander Diemand, Konstatin Arnold, Jürgen Kopp and Lorenza
Bordoli for their many contributions to the development and opera-
tions for the modeling platform. Furthermore, we are deeply
indebted to Jake V. Maizel Jr, Timothy N.C. Wells, Jonathan C.K.
Knowles, and Allan Baxter who have provided the necessary environ-
ment and resources during the various phases of this project. Finally,
we thank Stanley K. Burt, Robert W. Lebherz III, Karol Miaskiewicz
and Jack R. Collins of the Advanced Biomedical Computing Center
at the National Cancer Institute in Frederick Maryland for their sup-
port in operating the US mirror of the Swiss-Model server. We grate-
fully acknowledge the financial support by GlaxoSmithKline,
Novartis, the Swiss National Science Foundation, the Biozentrum of
the University of Basel and the Swiss Institute of Bioinformatics.
T. Schwede and M.C. Peitsch
vi Computational Structural Biology
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vii
2nd Reading
Contents
Preface v
Section I STRUCTURE PREDICTION 1
AND ASSESSMENT METHODS
Chapter 1 Protein Structure Modeling 3
T. Schwede, A. Sali, N. Eswar
and M. C. Peitsch
Chapter 2 Protein Fold Recognition and Threading 37
L. J. McGuffin
Chapter 3 Scoring Functions for Protein Structure 61
Prediction
Francisco Melo and Ernest Feytmans
Chapter 4 Assessment of Protein Structure Predictions 89
E. Capriotti and M. A. Marti-Renom
Chapter 5 The Biological Applications of Protein Models 111
A. Tramontano
Section II FROM STRUCTURE TO FUNCTION 129
TO DESIGN
Chapter 6 Evolution of Protein Folds 131
A. N. Lupas and K. K. Koretke
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Chapter 7 Classification of Protein Structures 153
A. Cuff, O. Redfern and C. Orengo
Chapter 8 Methods to Characterize the Structure 189
of Enzyme Binding Sites
A. Kahraman and J. M. Thornton
Chapter 9 Atomistic Simulations of Reactions 223
and Transition States
M. Meuwly
Chapter 10 Functional Motions in Biomolecules: 253
Insights from Computational Studies
at Multiple Scales
A. W. van Wynsberghe, L. Ma, X. Chen
and Q. Cui
Chapter 11 Protein-Protein Interactions 299
and Aggregation Processes
R. I. Dima
Chapter 12 Modeling and Simulation of Ion Channels 325
S. Bernèche and B. Roux
Chapter 13 Milestones in Molecular Dynamics Simulations 363
of RNA Systems
Y. Hashem, E. Westhof and P. Auffinger
Chapter 14 Computational Protein Design 401
J. G. Saven
Chapter 15 Prediction and Identification of B Cell 425
Epitopes Using Protein Sequence
and Structure Information
P. Andersen, D. Mkhailov and O. Lund
viii Computational Structural Biology
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Chapter 16 Computational Antibody Engineering 445
T. K. Nevanen, N. Munck
and U. Lamminmäki
Section III DRUG DISCOVERY AND 467
PHARMACOLOGY
Chapter 17 Small Molecule Docking 469
R. A. Friesner, M. Repasky and R. Farid
Chapter 18 Structure-based Pharmacophores and Screening 501
R. Lewis and R. G. Karki
Chapter 19 Molecular Dynamics-based Free 513
Energy Simulations
M. A. Cuendet, V. Zoete and O. Michielin
Chapter 20 Structure-based Computational Pharmacology 549
and Toxicology
Angelo Vedani and Martin Smiesko
Chapter 21 Structure-based Computational Approaches 573
to Drug Metabolism
M. A. Lill
Section IV NEW FRONTIERS IN EXPERIMENTAL 599
METHODS
Chapter 22 New Frontiers in X-ray Crystallography 601
C. U. Stirnimann and M. G. Grütter
Chapter 23 New Frontiers in High-Resolution 623
Electron Microscopy
A. Engel
Contents ix
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Chapter 24 New Frontiers in Characterizing Structure 655
and Dynamics by NMR
M. Nilges, P. Markwick, T. Malliavin,
W. Rieping and M. Habeck
Section V SELECTED TOPICS 681
Chapter 25 Docking for Neglected Diseases 683
as Community Efforts
M. Podvinec, T. Schwede and M. C. Peitsch
Chapter 26 Protein Structure Databases 705
D. Dimitropoulos, M. John, E. Krissinel,
R. Newman and G. J. Swaminathan
Chapter 27 Molecular Graphics in Structural Biology 729
A. M. Lesk, H. J. Bernstein
and F. C. Bernstein
Index 771
x Computational Structural Biology
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Section I
Structure Prediction and
Assessment Methods
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3
FA1
Chapter 1
Protein Structure Modeling
T. Schwede*,†
, A. Sali‡
, N. Eswar‡
and M. C. Peitsch§
1.1 Introduction
Knowledge of the three-dimensional (3D) structures of proteins pro-
vides invaluable insights into the molecular basis of their functions.
Furthermore, the design of experiments aimed at understanding
molecular mechanisms — such as site-directed mutagenesis, mapping
of disease-related mutations, and the structure-based design of spe-
cific inhibitors — are greatly facilitated by the detailed knowledge of
the spatial arrangement of key amino acid residues within the overall
3D structure. While great progress has been made in structure deter-
mination using experimental methods, such as X-ray crystallography
(Chapter 22), high-resolution electron microscopy (Chapter 23) and
*Corresponding author.
†
Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingel-
bergstrasse 50/70, 4056 Basel, Switzerland. E-mail: torsten.schwede@unibas.ch.
‡
Department of Bioengineering and Therapeutic Sciences, Department of
Pharmaceutical Chemistry, California Institute for Quantitative Biosciences (QB3),
University of California at San Francisco, Byers Hall at Mission Bay, Suite 503B,
1700 4th Street, San Francisco, CA 94158-2330, USA.
§
Novartis Institutes of BioMedical Research, Basel Klybeckstrasse 141, 4057 Basel,
Switzerland.
b587_Chapter-01.qxd 1/21/2008 2:44 PM Page 3
nuclear magnetic resonance (NMR) spectroscopy (Chapter 24),
these approaches are generally still expensive, time consuming, and
not always applicable. Currently, less than 50 000 experimental pro-
tein structures have been released by the Protein Data Bank PDB1
(Table 1.1), while another 3500 have been deposited but are still
awaiting release. These structures correspond to approximately
17 000 different proteins (sharing less than 90% sequence identity
among one another). Nevertheless, the number of structurally char-
acterized proteins is small compared to the 300 000 annotated and
curated protein sequences in the Swiss-Prot section of the
UniProtKB2
(http://www.expasy.org/sprot/). This number is even
smaller when compared to the 5.2 million known protein sequences
in the complete UniProtKB (October 2007). Even after removal of
the highly redundant sequences from this database (above), the
remaining 3.3 million sequences exceed the number of known 3D
structures by more than two orders of magnitude. Thus, no experi-
mental structure is available for the vast majority of protein
sequences. This gap has widened over the last decade, despite the
high-throughput X-ray crystallography pipelines developed for struc-
tural genomics.3–5
Therefore, the gap in structural knowledge must
be bridged by computation.
Computational methods for predicting the 3D structures of pro-
teins enjoy a high degree of interest and are the focus of many
4 Computational Structural Biology
FA1
Table 1.1. Current PDB Holdings (October 2007)a
Molecule Type
Proteins Nucleic Protein/NA
Acids Complexes Other Total
Experimental X-ray 36847 991 1709 24 39571
Method NMR 5929 788 134 7 6858
EM 106 11 40 0 157
Other 83 4 4 2 93
Total 42965 1794 1887 33 46679
a
The content of the table was obtained from http://www.pdb.org (1). EM: electron
microscopy.
b587_Chapter-01.qxd 1/21/2008 2:44 PM Page 4
research and service development efforts. The prediction of the 3D
structure of a protein from its amino acid sequence remains a funda-
mental scientific problem and it is often considered as one of the
grand challenges in computational biology and chemistry. Broadly,
four different types of approaches are commonly in use. The first and
most accurate approach is “comparative” or “homology” modeling
that uses experimentally elucidated structures of related protein fam-
ily members as templates to model the structure of the protein of
interest (the “target”). These methods can only be employed when a
detectable template of known structure is available. Second, fold
recognition and threading methods are used to model proteins that
have low or statistically insignificant sequence similarity to proteins of
known structure (Chapter 2). Third, de novo (or ab initio) methods
aim to predict the structure of a protein purely from its primary
sequence, using principles of physics that govern protein folding
and/or using information derived from known structures but without
relying on any evolutionary relationship to known folds. Finally, a
fourth group of methods, recently receiving a lot of attention, is the
“integrative” or “hybrid” methods that combine information from a
varied set of computational and experimental sources, including all
those listed above.
1.2 Modeling Methods
1.2.1 Comparative Protein Structure
Modeling Techniques
Template-based protein modeling techniques (aka “homology model-
ing” or “comparative modeling”) exploit the evolutionary relationship
between a target protein and templates with known experimental
structures, based on the observation that evolutionarily related
sequences generally have similar 3D structures. Most comparative
modeling procedures consist of several consecutive steps, which can be
repeated iteratively until a satisfactory model is obtained: 1) identifica-
tion of suitable template structures related to the target protein and
the alignment of the target and template(s) sequences; 2) modeling of
Protein Structure Modeling 5
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the structurally conserved regions and the prediction of structurally
variable regions; 3) refinement of the initial model; and 4) evaluation
of the resulting model(s).
1.2.1.1 Identification of modeling templates
and sequence alignments
Identifying suitable template structures and calculating an accurate
alignment of their sequences with that of the target are the key first
steps of the comparative modeling process. The sequence identity of
the target-template alignment is the most commonly used metric to
quantify the similarity between the target and template(s) and is also
a good predictor of the quality of the resulting model. It is thus cru-
cial to consider the target-template sequence identity level when
selecting template structures (Sections 1.2.2, 1.6 and Chapter 5), as
this will have a critical impact on the quality of the resulting model
and hence, its potential applications. The overall accuracy of models
calculated from alignments with sequence identities of 40% or higher
is almost always good (i.e. deviate by less than 2Å RMSD from the
experimentally determined structure) (Section 1.2.2). As the target–
template sequence identity falls below 30–40%, models that deviate
significantly from the average accuracy are frequent (i.e. deviate by
more than 2Å RMSD from an experimentally-determined structure).
Alignment errors also tend to rapidly increase in this regime and
become the most frequent cause of large errors in comparative mod-
els even when the correct template is chosen. Moreover, models based
on alignments with such low sequence identities may have an entirely
incorrect fold.6
While identifying and aligning sequences with similarities above
40% is relatively straightforward, more sensitive methods are needed
for the lower levels of evolutionary relatedness between sequences.
In recent years, significant progress has been made in the develop-
ment of sensitive methods for sequence homology detection and
alignment based on iterative profile searches, e.g. PSI-Blast,7
Hidden
Markov Models, e.g. SAM,8
HMMER,9
or profile-profile alignment
such as FFAS03,10
profile.scan,11
and HHsearch.12
Furthermore, in
6 Computational Structural Biology
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the absence of a detectable sequence similarity, fold recognition and
threading methods can be used to identify proteins with known
structures, that share a common fold with the target sequence
(Chapter 2).
1.2.1.2 Generating all-atom models
Comparative protein structure modeling yields an all-atom model of
a protein, based on its alignment to one or more related template
structures. Over the years, two commonly used approaches for model
building have emerged and can be described as follows: the first is a
rigid fragment assembly approach, in which an initial model is con-
structed from structurally conserved core regions of the template and
from structural fragments obtained from either aligned or unrelated
structures.13,14
The initial model is then subjected to an optimization
procedure to refine its geometry and stereochemistry (Section 1.2.1.3).
The second approach relies on a single optimization strategy that
attempts to maximize the satisfaction of spatial restraints obtained
from the target-template alignment, known protein structures, and
molecular mechanics force-fields.15
Such an approach may not require
a separate refinement step. However, most model building proce-
dures are usually followed by the application of specialized protocols
to enhance the accuracy of the non-conserved regions of the align-
ment such as loops16,17
and/or side chains.18,19
1.2.1.3 Model refinement
Once an atomic model has been obtained, it can potentially be refined
to idealize bond geometry and to remove unfavorable contacts that
may have been introduced by the initial modeling process. The refine-
ment will generally begin with an energy minimization step using one
of the molecular mechanics force fields.20,21
For further refinement,
techniques such as molecular dynamics as well as Monte Carlo and
genetic algorithm-based sampling methods22–24
can be applied. For
instance, in certain cases molecular dynamics has been reported to
yield some improvement of side chain contacts and rotamer states.25
Protein Structure Modeling 7
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b587_Chapter-01.qxd 1/21/2008 2:44 PM Page 7
Monte Carlo sampling with focus on regions most likely to contain
errors, while allowing the whole structure to relax in a physically real-
istic all-atom force field, can significantly improve the accuracy of
models in terms of both the backbone conformations and the place-
ment of core side chains.26
Nevertheless, limitations still exist in sam-
pling as well as force field accuracy.
1.2.1.4 Model evaluation
Model evaluation aims to recognize the various problems that might
have occurred during the modeling process. Furthermore, estimating
the overall geometrical accuracy of the individual regions of the
model is an essential task of model evaluation. There are two kinds of
evaluation schemes that are commonly employed. The first is “fold-
assessment” that seeks to ensure the calculated models possess the
correct fold and helps in detecting errors in template selection, fold
recognition, and target-template alignment.6,27–29
The second class of
methods seeks to identify the model that is closest to the native struc-
ture out of a number of alternative models.30–37
A combination of
such assessments is usually employed to select the most accurate
model from amongst a set of alternative models, generated based on
different templates and/or alignments. In general, addressing these
different types of assessment requires specialized scoring systems and
classifiers (Chapters 3 and 4).
1.2.2 Accuracy and Limitations of Comparative
Protein Structure Modeling
Comparative protein structure modeling relies on the evolutionary
relationship between the target and template proteins. Consequently,
the application of this approach is limited by 1) the availability of
suitable template structures; 2) the ability of alignment methods to
calculate an accurate alignment between the target and template
sequences, even when the relationship between them is remote;
and 3) the structural and functional divergence between the target
and the template.38
8 Computational Structural Biology
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The percentage of sequence identity between target and template
correlates with model accuracy and often allows for a good first esti-
mate of the model quality. As a rule of thumb, comparative models
based on more than 50% sequence identity to their templates can be
considered as “high accuracy models” and tend to have about 1 Å
root mean square deviation (RMSD)38
for the main-chain atoms,
which is comparable to the accuracy of a medium-resolution NMR-
derived structure or a low-resolution X-ray structure.5,39
Inaccuracies
are mainly found in the packing of side chains and loop regions.
Comparative models based on 30 to 50% sequence identity can be
considered “medium accuracy models”, where the most frequent
errors include side-chain packing errors, slight distortions of the pro-
tein core, inaccurate loop modeling, and sporadic alignment mistakes.
Since alignment errors increase rapidly below 30% sequence identity
and become the most substantial origin of errors in comparative mod-
els, comparative models based on less than 30% sequence identity are
considered “low accuracy models”.
1.2.2.1 Template availability and structural diversity
It has been observed that a very small number of different folds
account for the majority of known structures,40
and a recent study
has argued that most sequences could already be modeled using
known folds (or fragments of known folds) as templates.41
Thus, for
the majority of target protein domains, a structure with a similar fold
would be available within the Protein Data Bank (PDB). However,
models based on alignments with low sequence identity often pro-
vide accurate information only about the fold of the protein. As
stated above, the accuracy of homology models decreases rapidly
when the sequence identity between the target and template drops
below 30%, mainly due to alignment errors and our inability to
model structural differences between the target and the template.
While the overall fold of proteins is often well conserved even at
undetectable levels of sequence similarity, protein function — such as
enzyme function and specificity — shows much higher variability,42,43
even at high levels of sequence identity (above 50%). New methods
Protein Structure Modeling 9
FA1
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Discovering Diverse Content Through
Random Scribd Documents
Computational Structural Biology Methods and Applications 1st Edition Torsten Schwede
Computational Structural Biology Methods and Applications 1st Edition Torsten Schwede
Additional proofs of the Cleland ornaments were sent immediately to
Mr. Rogers in London. With them he made eight designs, cutting the
proofs and pasting the ornaments to show the desired effect. This
tree, for instance, was used on the title page of the Barnacles insert:
This was printed from a line engraving made direct from Mr. Rogers'
paste-up, and used "as is" to show how accurately his layouts for
this type of work reach the composing-room.
A month later, in May 1931, Mr. Rogers returned his layouts with this
note: "... I have only just been able to complete the designs I had
begun.... One or two other combinations occurred to me, which I
have also put in—but we could go on endlessly, almost, when once
started on this kind of thing.... I would have built up the designs
with impressions from sections of a slug, had you sent an inch or
two of each unit; but it is perhaps better, though slower, to cut and
paste proofs, as each cutting is a guide to the compositor as to how
and where trimming or beveling the ornaments are necessary. But
only a few such trimmings are required, and all the bevelings are at
45 degrees—as is the diagonal composition of the oak tree heads.
"If at all possible I would like to have a chance to revise proofs of
these, before they are actually printed—but if that isn't feasible, then
I must rely on the compositors getting the closest possible
approximation to my pasted-up designs. As close setting as possible
is the secret of most work of this kind. The various parts must hang
together well—though I do not mind a slight indication at the joints
that they are made of individual pieces of type. I once had an over-
zealous electrotyper fill up all the joints with solder—and ruined the
appearance of the design—it looked like a drawn one."
It wasn't possible to show Mr. Rogers what had been done with his
layouts for the insert in Barnacles, which was essentially a surprise
book distributed as a keepsake at a dinner in his honor.
The "fighting cocks," to cite one instance, were originally suggested
by B.R. to be used to dress a page folio at the bottom of the page;
in the insert they were raised to the top of the page and printed with
his initials. Other slight adaptations of similar character were taken
in that piece of printing.
"Typographic whimsy," wrote Carl Purington Rollins in B.R.—
America's Typographic Playboy, in 1927, "is a pretty difficult
achievement. The compositor at the case is too much concerned
with the practical minutiæ of his craft to have much time for such
trivialities, and the man who designs printing at a draughting board
is apt to find his humor, if he attempts it in type, limping like a
thrice-told jest. Mr. Rogers has had the advantage of enough
familiarity with type to know what can be done, and he has been
able at times to work with compositors who take a large and robust
view of their calling."
That "whimsy" Mr. Rollins had reference to lies in many of B.R.'s
more ephemeral efforts, frequently reproduced. It is reflected to a
measure, by The Symbol and the Saint page. But there is
considerably more than whimsy in the type ornament designs by
B.R. These have graced dozens of books of varying subjects ... and
the marvel of it all is, to me, that the man never repeats himself—he
swings off on a new tack ... adventurous, exploring, mastering new
trails, scattering typographic inspiration for dozens of others,
pointing up paths they previously never even suspected.
Postscript, 1951: It is fitting to add a note concerning one of B.R.'s
more distinguished recent projects, the great folio Bible designed for
The World Publishing Company, which was four years in the making.
The design of the World Bible employed decorative treatment for the
bordered title page, the sixty-six book openings, initial letters and
numerous tailpieces. "These, together with the type selected [a
revised, special cutting of Goudy New-style], are intended to give a
slightly oriental flavor to the volume," B.R. pointed out, "indicative of
the Syriac and Hebrew sources of the text on which the King James
translators based their classic version."
In discussing the matter of ornaments in the Bible with the
publishers, B.R. revealed his thinking concerning their use: "... Most
of the Books will probably not begin at the top of the page and the
use of ornaments are to me necessary to separate the end of the
preceding book from the title of the following one.
Computational Structural Biology Methods and Applications 1st Edition Torsten Schwede
"The Bible has always been a book on which much decoration and
illustrations have been lavished, and there is no reason in tradition
why it should be treated solemnly in that respect. The very first
edition (of which I have specimen sheets and a whole Bible printed
from the same type and with the same decorations by the same
printer, twenty-five years later, 1635) is just peppered with woodcut
decorations and type ornaments. So we have a good precedent for a
decorated treatment—if any were needed. You know the Bible is on
the whole one of the most exciting texts in existence, and the
modern 'practical' treatment of it as mainly a book of devotion is
ignoble, to say the least...."
Some of the typographic decoration and initials used in the Bible are
included here. William Targ's detailed account, The Making of the
Bruce Rogers World Bible, contains most of the decorative elements
—initials, tailpieces and chapter initials—and reveals the intimate
story of the progress of the book's production through the four
years. It was published by World in 1949, in a limited edition of 1875
copies, 500 of which were for sale.
COMPOSED IN CENTAUR AND ARRIGHI TYPES
Book labels devised with typographic ornament by B. R.
In the originals, a second color was used for each
excepting the Reydel.
SOME TENDENCIES IN MODERN
TYPOGRAPHY
Daniel Berkeley Updike
From Some Aspects of Printing Old and New by D. B. Updike. Copyright 1941 by
the author. Reprinted by permission of the Providence Public Library, Providence,
Rhode Island.
Not very long since I was asked by a printer to what extent he
should accept or avoid modern trends in the design of types and
books. I attempt here to answer that question.
I have a friend, connected with one of the great companies
supplying machines for type composition. Not long since he spoke to
me in unflattering terms of the examples of typography shown at an
exhibition of the products of the Bauhaus School, originally of
Weimar and later of Munich. He protested against a practice there
manifested of discarding capital letters and depending solely on
those in the lower-case. I consoled him by showing him a French
book, printed entirely in this style. This volume, entitled Typographie
Économique, was published in Paris in 1837 and so far as it had any
influence on printing, then or later, is as dead as Queen Anne. The
author, the Count de Lasteyrie, who promoted this scheme, was one
of a race of French scientists, of some intellectual and social
importance—one of the daughters of Lafayette married into that
family. In the eighteenth century no less a person than the German
writer Grimm tried a similar typographical plan. In the Fairy Tales
containing "Snow White and the Seven Dwarfs," later compiled by
Jacob and Wilhelm Grimm, the practice was not continued. This
supports the contention that many new and disturbing experiments,
under the patronage of distinguished names, are merely survivals or
revivals of ancient failures. Thus in the light of experience, there is in
Bauhaus typography nothing for my acquaintance—or anybody else
—to be excited about.
Now Bauhaus typography is of the essence of modernism. That its
position may be fairly stated I quote the following from a Bauhaus
Year Book:—verbatim and (I may add) literatim:
["] why should we write and print with two alphabets?
both a large and a small sign are not necessary to indicate
one single sound.
A = a
we do not speak a capital A and a small a.
we need only a single alphabet. it gives us practically the
same result as the mixture of upper and lower-case
letters, and at the same time is less of a burden on all
who write—on school children, students, stenographers,
professional and business men. it could be written much
more quickly, especially on the type-writer, since the shift
key would then become unnecessary, typewriting could
therefore be more quickly mastered and typewriters would
be cheaper because of simpler construction, printing
would be cheaper, for fonts and type cases would be
smaller, so that printing establishments would save space
and their clients money. with these common sense
economies in mind ... the bauhaus made a thorough
alphabetical house-cleaning in all its printing, eliminating
capitals from books, posters, catalogs, magazines,
stationery and even calling cards.
dropping capitals would be a less radical reform in english.
indeed the use of capital letters occurs so infrequently in
english in comparison with german that it is difficult to
understand why such a superfluous alphabet should still
be considered necessary.["]
Now in German printing all nouns have capital letters. In the
sentence "A Dog chases a Cat into a Barn," dog, cat, barn are all
capitalized. No one can be blamed for wanting to be rid of so much
capitalization. But when Germans purge anything the innocent
invariably suffer with the guilty. Thus all capitals must go. While it
may have overcome a difficulty felt in Germany, this imported
missionary zeal corrects no difficulty in the printing of English prose
or poetry. In some instances such a custom brings about surprising
results. Suppose, for example, a newspaper says "the white house
favors black and prefers even green to a dyed-in-the-wool red." To
make the sentence intelligible would need the addition of a number
of words—which would not be typographie économique! We need
labour this point no further but leave these experiments to the
advertising of Coty and Elizabeth Arden. Such effects have what is
called attention value—like Neon signs—but I am not considering
that kind of typography. I have, however, here traced the source of a
current fashion of printing signs and advertisements without capital
letters.
I have been classed by my work as a conservative, but I am a liberal
conservative or a conservative liberal—whichever you like or dislike.
All I wish to conserve, either in traditionalism or modernism, is
common sense. What little I have was gained by experience. I
regard many typographic experiments with good will and many
traditional viewpoints with tolerance. I agree wholeheartedly with
neither. I remember—or try to do so—that every generation has in
turn to be told that there was once a man named Caesar, who wrote
a very dull book called the Commentaries, of which the first
sentence is all that most people remember; that the makers of
Baker's Chocolate did not invent the familiar picture of a chocolate
girl, which was an eighteenth-century painting by Jean Etienne
Liotard now in a Dresden picture gallery, and that William Blake did
not write, but only illustrated, the Book of Job. We who have long
known these things forget that people are born not knowing them.
We should therefore look tenderly on many typographic
experiments. To us elders they may seem akin to lighting a fire with
kerosene or applying one's tongue to metal in zero temperatures,
but it is by such unwise ventures that we outgrow them. And as I
have spent a long life learning, and to most questions do not yet
know the answers, I have no right to frown on more youthful and
enterprising enquirers.
Obviously some of the eccentricities of present-day typography are a
natural reflection of that rather tortured world in which we find
ourselves. If art, the drama, literature, and music reflect current
trends of life it is natural that printing should in a measure do so. If
we throw overboard old standards of conduct, we may far more
readily throw over old standards of taste. When one casts a
convention away as useless and outmoded, we often learn for the
first time why it was there! It is urged that fuller expression of
individuality, unhampered by rules, is development. It seems to me
more accurate to say that through the experience of trying these
experiments development comes—though not always of a kind
expected. Such development ought never to stop until in the exact
sense of the word we are "accomplished"—finished—which few live
to be.
The problem is to distinguish between a true development, and a
false one. In judging either modernistic or retrospective typography,
that is what must be decided. Do these developments—wise or
otherwise, produce a well-made and readable book—in short a good
book? "In the printing of books meant to be read," says an authority,
"there is little room for 'bright' typography. Even dullness and
monotony in the type-setting are far less vicious to a reader than
typographical eccentricity or pleasantry. Cunning of this sort is
desirable, even essential in the typography of propaganda, whether
for commerce, politics, or religion because in such printing only the
freshest survives inattention. But the typography of books, apart
from the category of narrowly limited editions, requires an obedience
to convention which is almost absolute—and with reason."
It is the fashion, just now, to decry typographic conventions. Some
conventions and traditions deserve to be decried and some have
already been laughed out of existence. There are, however, good
and bad conventions and traditions in printing, just as there are true
and false developments, and the trick is to know which is which!
Convention and particularly tradition are, generally, the crystallized
result of past experiments, which experience has taught us are
valuable. In some of the extreme modernistic typography a little
more tradition might come in handy. The trouble with the modernist
is that he seems afraid not to throw everything overboard and
mistakes eccentricity for emancipation. Thus some books of today
seem to be the arrangement of a perverse and self-conscious
eccentricity. Such printing is often the work of eager, ambitious, and
inexperienced men, and because they are young and God is good,
one can afford to be patient; sure that they will, in the long run,
outgrow the teething, mumps, and measles of typography. Their
convalescence will possibly be hastened by meditating on the saying
of Lord Falkland that "when it is not necessary to change, it is
necessary not to change."
No movement ever accomplishes all that its first promoters intended
or hoped for; almost all movements make some lasting contributions
to our common stock. Every new idea, every new invention brings
along with its expected benefits unforeseen evils. Modernistic
architecture is at present exciting because new and unusual; when
more common it will become commonplace. When it becomes
difficult to differentiate the exterior of a modernistic church from a
warehouse, we may get very, very tired of it. Then a compensating
reaction will set in and balance will be restored. The same thing is
true of modernistic typography. At present, it shocks us into
attention, but we get tired of being shocked, for we do not want
printing to surprise but to soothe us. The modernist must remember,
too, that "such a thing as an underivative work of art does not and
cannot exist, and no great master in the arts has thought or
asserted otherwise." We gladly admit that some modernistic
formulas have had good results. In architecture, perhaps to some
degree in typography, they have taught us to get rid of clutter and
useless ornamentation. But neither the one nor the other leads
anywhere—except to a dead end.
The conservative, however, need not think that all truth is on his
side. However much he tries to practise retrospective or "period"
typography, consciously or unconsciously his work will show the
influence of his time. Just as there is a popular idiom in speech
which varies in each decade, so there is a current idiom in printing.
All these idioms, literary and typographic, have not come to stay, but
some become accepted terms. Under Theodore Roosevelt we
suffered from the word "strenuous." President Harding inflicted the
word "normalcy" on American speech. We now have "reactions," and
"contacts." Clergymen "challenge" things, have "spiritual
adventures," talk of "strategic positions" for their parish houses and
aid parochial charities by "clarion calls," though if confronted with a
"clarion" (if this instrument exists outside of sermons) they would be
quite unable to blow it. All these catch-words and stock phrases are
in the air. We suffer much the same thing in typography, about
which there is also a new jargon which replaces the old clichés of my
youth about rhythm, balance, and colour. Neither in speech nor
printing can one make a clean sweep of the past nor help being of
the present, no matter how hard one tries. I deplore violent
attempts to make current printing accord with the spirit of the age.
It always has, always will, and does now.
Nor need the conservative sniff at typographic experimentation. To
turn to another department of daily life, what would happen if no
one had ever tried experiments with food? In the distant past there
was the first human being who—as an experiment—ate an oyster,
though perhaps first trying jelly-fish with less comfortable results.
Others died of eating toadstools before people learned that they
could survive on mushrooms. Almost all our vegetable food we owe
to gastronomic adventurers. Thus the hide-bound conservative owes
sustenance to the fruits, and vegetables, of experiment.
To speak more seriously, both modernist and conservative should lay
to heart what Benedetto Croce says in his Autobiography about "the
impossibility of resting on the results of past thought" and the
necessity of modesty in stating one's present position. "I see," he
writes, "a new crop of problems springing up in a field from which I
have but now reaped a harvest of solutions; I find myself calling in
question the conclusions to which I have previously come; and these
facts ... force me to recognize that truth will not let itself be tied
fast.... They teach me modesty towards my present thoughts, which
tomorrow will appear deficient and in need of correction, and
indulgence towards myself of yesterday or the past, whose thoughts,
however inadequate in the eyes of my present self, yet contained
some real element of truth; and this modesty and indulgence pass
into a sense of piety towards thinkers of the past, whom now I am
careful not to blame, as once I blamed them, for their inability to do
what no man, however great, can do ... to fix into eternity the
fleeting moment."
There is, to the reasonable mind, no real quarrel between
modernism and traditionalism in printing, except in degree.
Modernism must and does influence the conservative in spite of
himself—if by modernism we mean a healthy awareness of the
needs of the time in which we are living. Tradition must and does
influence the modernist, if by tradition we mean patient and
respectful appraisal of what that accumulation of yesterdays, which
we call the past, has to teach. It is only by experience that we can
effect a wise blend of the two. Then we produce books which, while
representing the best practice of our time, will outlast it. The
appraisal of their ultimate values we must leave to the future.
"There is no past that we need long to return to," said Goethe,
"there is only the eternally new which is formed out of enlarged
elements of the past; and our real endeavor must always be towards
new and better creation."
COMPOSED IN BELL TYPES
PETER BEILENSON
The Amateur Printer:
HIS PLEASURES AND HIS DUTIES
From Graphic Forms: The Arts As Related to the Book. Copyright 1949 by Harvard
University Press. Reprinted by permission of the publisher.
Although the title of this piece is sufficiently long to be impressive
and important-sounding, all I really want to write about is printing as
fun. I am going to write about the amateur printer, and the amateur
is the fellow who has fun.
I do not wish to belittle the affection a professional printer may have
for his work. He should love his work. But he can love it only in a
different way: for after all he is essentially a businessman about it.
His work, like that of any other businessman, is something he has to
sit down to by nine in the morning and something he can't leave
until five at night. It is something that involves landlords and labor
unions, payrolls and tax inspectors, truckmen, office-boys, salesmen,
compositors, pressman, bindery workers—and customers. He has to
worry about payments, and depreciation, and publicity, and time
sheets.
The professional has to concern himself with all these things which
are not printing at all, because he is in business and has to make
money. His primary yardstick of success as a professional is: How
much money did we make last year? Of course he has other minor
yardsticks of success too: he may be successful because his presses
turn out useful things like timetables, or gratifying things like
corporation reports for the year, or beautiful things like four-color
reproductions of Varga girls. To make these things well is a kind of
fun; and insofar as the fun comes from the satisfaction in the thing
itself rather than in the profit that derives from it, I'd like to call it
amateur satisfaction.
But essentially our professional printer—and permit me to limit
myself to the professional book printer—is supposed to make money,
not to have fun. And he makes money best, nowadays, if his plant is
equipped with the efficient modern machinery which is designed for
maximum production. Such machinery is a wonderful creation of
man; it is thrilling to watch in action; and it gets results. But it has
its disadvantages. Now that mechanization is becoming more and
more complete in more and more places, we can begin to see clearly
the greatest disadvantage of all: under such mechanization
individual workers have lost pride and satisfaction in their work,
because they have become mere replaceable units of less and less
importance; whereas the machines they operate are more and more
important, and have become the essential units.
A generation ago the professional printer might have boasted of his
skilled compositors, who could set type more expertly, or his skilled
pressmen, who could make more careful overlays or match ink
better than someone else's craftsmen. Today he boasts of his
remote-control composing machines, his presses which come close
to eliminating make-ready altogether, and his ink supplier's new
gadget which matches colors scientifically. Today the most successful
printer is the one who with the least possible dependence on man-
power, can keep the most presses running fastest for the greatest
number of hours per day and days per year. He is not the one with
the most skilled craftsmen.
In such a world, where the executive's function is to feed the
machine and the workman's is to tend it, the human spirit begins to
cry out for the fun in work which I have called the amateur
satisfaction. It is true that today's shorter working hours—which the
machine makes possible—permit people to have more outside fun;
permit the manager to play more golf, and the workman to play
more softball (or more pinball) in the late afternoon; it is true that
more people now see more beer advertised on more television
programs, and may even drink more of it, in the evenings. But
managers and workmen alike turn so avidly to such kinds of fun
because they no longer get fun out of their daily work. It is
becoming harder and harder for people to equate work and
happiness.
Now I do not set myself up as a social reformer dedicated to the
dream that all people should be happy in their work. Nor do I
propose as a step to this end that we revert, smash the wonderful
machines, and go back to the good old days when everyone really
did work with his hands—usually from dawn to dark, six days a
week. There was no pinball or television then, but still I do not wish
to go back! Nor do I suggest that the solution is the promised thirty-
hour week, with all the workmen driving their own Buicks home at
two each afternoon, and taking out the wife and kiddies to Braves
Field or the Gardner Museum.
But I do suggest that some of you people who really love printing,
but are too involved with the nine-to-five daily business of it to enjoy
it much, should enrich your lives by becoming amateur printers in
your spare time. You will have fun.
I yield to no man in my boredom with vegetables and salads. I see
green at every meal save breakfast. I have eaten enough
stringbeans to stretch—if they were straightened out and laid end to
end—from Fordhook Nurseries in Delaware to the city of Burbank,
California. If you could see all the lettuce leaves I have consumed in
my lifetime, piled leaf on leaf and dripping in their oils, their vinegar,
their mayonnaise, and their roquefort dressings, you would be
absolutely appalled. But, bored as I am with green things on the
table—bored because despite their goodness they have been too
plentiful and too easily come by—I am not bored on those occasions
when, like Candide, I cultivate my garden, get my hands into the
dirt, and smell God's good fragrance in the loam. To watch the
power of living things like salad greens and stringbeans pushing
their way out of the seed, up through the earth, reaching down for
water and up for sunlight with an irresistible drive, is to realize
afresh the power of life on this planet. It is a reinvigorating and
religious experience. It is impossible to watch seeds grow into plants
and flowers and fruit and still to believe cynically in a mere
mechanistic explanation for such a life drive. To get back to the
seed, the earth, and the root is to re-experience the fun and
meaning of life.
In the same way that I have become bored with salad, we have all
become bored with words, printed words. We have seen too many of
them, we have read too many of them, we have measured, or
proofread, or edited, or sold, too many of them. We have forgotten
their primal power, their irresistible living urge. We have forgotten
that sincere authors have not put them down on paper because of
two cents a word or 10 per cent of the retail gross—that they have
been written (in the best cases) out of human necessity, human
ebullience, human passion, human sympathy, or human
understanding. The industrial book-printing world cannot ever think
of words in that way. It must always think of them as areas of type
22 by 28 picas, as numbers of pages which do or do not make up a
multiple of thirty-two, as units of sale at $3.00 less 40 per cent.
To go back to nature and become an amateur printer in such an
industrialized book world is like working in the garden when you are
bored with salad. You really get back to the roots of words. If you
are a genuine amateur printer, and set the type and print the pages
yourself, you actually can share in the creative agonies and
satisfactions of the author. For you put down his words, letter for
letter in your type-stick, just as he did with his quill or his battered
Remington. The best way on earth to appreciate an author and his
creative spirit (or for that matter to realize more quickly the faults in
him) is to pick him up letter by letter from a California case. An even
more acid test is to distribute the type after printing him. In such a
case you pick up half a dozen lines of type at once and work
backwards, distributing the last word of the last line first. It is a
revelation how the hollowness of an author can show up under this
treatment. It is especially cruel to poets, for every word which is not
really necessary, which is there just for padding or for a rhythm or a
rhyme, becomes as noticeable as the well-known sore thumb. But
the genuine, sincere author with a pure style stands up beautifully
under such treatment, and has his reward in your pleasure at this
discovery.
After you have set your author's type you must make up his pages,
choose his decorations or illustrations, and set his headings. You
must decide whether to stretch him to twenty-four pages or
condense him to sixteen. You must buy his paper, lock up his pages
in your chase, make him ready, curse your press which is printing
him, apply your ink to his words, and impress him for posterity.
Perhaps you will thereafter fold him, sew him, and encase him in
boards.
In so doing, you become, to the extent of sixteen or twenty-four
pages, in an edition of one hundred or three hundred copies, God.
You have created something which did not exist before, and which
would not have existed save for your thinking brain and tired back
and dirty hands. True, you have not created Heaven and Earth, and
you have undoubtedly worked at your creation for more than the
original quota of six days. But anyway you have given the world
something which was at first only words you loved, and is now a
whole, real book, which you love all the more because it is your
book, your child, your embodiment of those words. That is the fun
and satisfaction of being an amateur. In our printing world there is
no other satisfaction equal to it.
Good old Ralph Waldo Emerson was mortally right when he wrote
down his doctrine of Compensation. His doctrine of Compensation
says that every pleasure carries some penalty, every gain some kind
of loss. Every duty accepted gives you a satisfaction, and every
satisfaction received involves you in a duty. Thus far I have written
of the satisfaction of your being an amateur printer. Now I wish to
write of your duty and obligation.
The amateur book printer has a duty which, if he will accept it, will
in the long run return to him the greatest satisfaction. This duty is to
teach the professional, by example, about the outer cultural world,
and to experiment for him in matters of printing style. Now this is
directly contrary to what ninety out of one hundred current amateurs
would seem to think, and I must therefore beg their ninety pardons
if I disturb their habits of mind.
Most amateurs either don't trouble their minds about problems of
printing style at all, or else they fall too easily into the habit of
working in the Colonial style, or Venetian style, or some other
historical style, rather than in a contemporary one. Maybe they do so
for psychological reasons. And maybe not. I am too set in my diction
to learn the trick of talking in psychological terms. I would express
their case like this: Amateurs who work in historical styles do so
because they are romantics, romantics who turn away from the
impersonal machine world of the present for a breath of the more
human and glamorous-seeming past. I sympathize with such an
instinct, and hold myself ready to defend any man who seeks to re-
inject a human element into the printing craft.
The trouble is, such amateurs think that because printing in the past
was done by hand, and because there is something more satisfying
and human about printing by hand, they must therefore work in an
antique printing style and make Colonial and Venetian books in order
to enjoy themselves. This is a false syllogism. I strongly recommend
printing by hand to amateurs because it will give them greater
satisfaction, not because it will make their books look like antiques.
It is too easy to fabricate such antiques, and to do so will in the long
run give you less enjoyment than making something which in style is
original and new.
As a matter of fact it is already too late to think in terms of revivals
and reproductions. In printing, the revival habit started over a
hundred years ago with Whittingham and Pickering, when they
dusted off the forgotten Caslon types and the eighteenth-century
style. It has been going on ever since, and reached a climax of
understanding and skill in our century at the hands of Updike,
Rogers, Rollins, Goudy, and others. This revivalism was a kind of
search for humanism, and a kind of rebellion against commercialism.
These men were not unique. In every generation since 1800, in
every art and craft, every field of thought, the Industrial Revolution
has prompted men to make the same search backward for
satisfactions which the modern world did not seem to offer.
Too many of our amateurs are still making the same search,
although the Industrial Revolution is well over one hundred years
old, all the necessary backward searching has been done, and all the
historical styles have been reworked. Our predecessors have made it
unnecessary for us to go through the process once again. We can
see now that their work was an escape perhaps for them, but that it
can never be a durable way of creative realization for us. From now
on, we must join up with the forward-looking crowd who think they
can build a new world.
The book-printing industry has not been very forward-looking in
matters of style. With the exception of a few printers and designers,
book printers have been unhealthily backward. Therefore the time is
ripe for amateur book-experimentalists to prod and teach them. The
amateur can do it.
He is, or should be, a man with interests in other fields of culture
than his own. He is aware already of what has been done in painting
and music, in fabrics and furniture design, in architecture too—most
important of all. He must now help printing to develop its own new
styles, equivalent to those in other fields. That he can do so is
evidenced by the fact that in recent years the greatest strides
forward have been taken not by the professionals but by people who
in a sense are amateurs, but who have known how to apply modern
ideas from other fields.
The Bauhaus group first became notable, between the wars, by
applying the functional theories of modern architecture to the
printed page. The Black Sun Press and Harrison of Paris applied the
ideas of Monroe Wheeler and others who were stimulated by
modern painting. There may be similar publishing projects in this
country today, but they are not yet influential. The most effective,
most vocal, most lovable of contemporary American influences is
that rugged individual Merle Armitage, whose ideas have been
influential in shaping my own attitude. Such people all know that the
world has changed; that it will never turn back again; and that it is
up to us to catch on to the flying coattails of Today. I urge other
amateurs to join the ranks of these apostles of change. It will be a
great day for all of us when ninety out of one hundred are
experimentalists, and not the other way around.
Of course in urging amateurs to develop new styles, I am not
recommending any easy hobby. It is simple, but dull, to copy an old
style. It is hard, but exciting, to work out a new one. And while you
are working at it, you must expect cynical observers to give your
experiments the adjective "wacky"; you must expect certain curious
kinds of people to praise your work for the wrong reasons; and you
must expect alternating moods of conceit and frustration. The proofs
you gloat over at night will become commonplace by dawn. Your
wife may go back to her mother in rage and despair. You may need
sleeping pills.
You will make misjudgments about the intelligence of ordinary
readers. You will make mistakes of taste. You will find it too easy to
get an effect by means of shock, and you will forget that any book,
even a twenty-first-century book, must be a coherent unit. And you
will often, since there are no highway markers for the explorer, feel
lonely and discouraged, and want to go back to the old familiar well-
traveled roads again.
But if you go through with it, or even if you just play with it
sometimes as a hobby, you can have great fun. For it will put you
out in the open, free to please yourself, with the boss and the
customer left far behind. You can be subtle or bold, as you feel the
urge, for you do not have to please the great common denominator,
the common man. You can advance your own work by looking to
other fields of creation, enjoying and profiting by the experiments
going on in them. You can feel yourself a part of the whole forward-
looking culture of your day, and not someone off in a little forgotten
corner.
And, if you do strike a vein with the glitter of real gold in it, you will
become rich indeed. For you will have become a creator in a new
sense; your duty done as an amateur will be compensated with a
twenty-four-carat satisfaction. At such a moment of realization you
will have earned the privilege to rest and feel content. As on a
seventh day after six of creation, standing late at night with
bloodshot eyes and inky fingers and aching back in a paper-littered
room, you have become a creator. You have not merely escaped
from the flattened monotony of the machine age—you have become
one of the shapers of its future. More power to you in that work!
T. M. CLELAND
Harsh Words
An address delivered at a meeting of The American Institute of Graphic Arts, in
New York City, February 5th, 1940, on the occasion of the opening of the
eighteenth annual exhibition of the Fifty Books of the Year. Copyright 1940 by T.
M. Cleland. Reprinted by permission.
Mr. Chairman and Members of The American Institute of Graphic
Arts:
The generosity of your invitation to me to speak on this important
occasion leaves me a trifle bewildered. I am so accustomed to being
told to keep my opinions to myself that being thus unexpectedly
encouraged to express them gives me some cause to wonder if I
have, or ever had, any opinions upon the graphic arts worth
expressing. But since it is the theory of your Committee that I have,
and it may never be anybody's theory again, and they have gone so
far as to give me no instructions or suggestions as to the scope or
the limitations of what I might say, it would seem as ungracious to
decline such an exceptional offer as it would be to abuse it. So if I
accept it as wholeheartedly as I believe it was given—if I take you at
your word and say things that I have long wanted to hear somebody
say—I hope it will not be thought an abuse of this kindly tendered
privilege.
I realize that, nominally at least, my subject must be that of printing
and typography as exemplified by the selection of the fifty best
books of the year which we are here to celebrate; and I suppose, by
comparison to deplore the fifty thousand worst books which may be
seen elsewhere. But by what may seem a very odd paradox, I don't
quite know how to stick to this subject without wandering a good
way off it. Or, perhaps I should say that I cannot approach it directly
except by a very roundabout way.
If I have a thesis for these remarks, I can only develop it in terms of
a tree. This is because I do not believe that invention in the arts can
be picked from empty space like objects in a prestidigitator's act.
Fruits really grow on trees and trees have roots in the earth. The
tree I have in mind is cultural civilization: one of its limbs is art and a
branch of this we call the graphic arts, and a twig on this branch is
printing and typography. I promise not to dig into the roots of this
tree, but I may be found, monkey-wise, climbing all over it before I
am through.
I am at some disadvantage in that I do not belong to any
organizations for the advancement of typography and the graphic
arts—not even to this one—and I am ill-informed and out of touch
with what is going on in these fields except by casual observation.
But as members of this very useful organization, you are not
engaged in printing or other graphic arts, I take it, solely for each
other, but for the enjoyment and delectation of the world at large.
So there is a partially compensating advantage in my being "at
large" myself, and thus able to speak of present trends in the
graphic arts as they appear from the outside, looking in. But this
advantage may in turn be offset by the fact that I cannot honestly
speak of what I see with much enthusiasm. I can bring you no
message of hope or light of inspiration. Much as I am filled with
admiration and respect for many individual talents and
accomplishments that still contrive to exist, they seem to me to
stand unhappily isolated in what I can't help viewing as artistic
bankruptcy and cultural chaos. Among them are printers making
beautiful books and other things about as well as these things have
ever been made. But as to the general volume of printing, no one
has asked me, to be sure, what I thought was the lowest point of
artistic taste in the five hundred years of its existence which we are
celebrating this year, but if anyone should ask me, I would be bound
to say that we have reached that point just about now. Things may
get worse, but it's hard to see how they can. To paraphrase a
remark in the concluding chapter of Updike's classic work on printing
types, it has taken printers and publishers five hundred years to find
out how wretchedly books and other things can be made and still
sell.
I am not forgetting that there were some very benighted periods of
taste in other centuries that would seem to refute this sweeping
assertion. Perhaps it is worth noting here—and the fact is peculiarly
ironical—that the design and style of official and governmental
things—money, postage stamps, bonds and stock certificates—was
created and solidified into a seemingly unalterable convention at that
hitherto all time low point of the decorative arts in the mid-
nineteenth century. So powerful is this convention that we would be
suspicious of a ten dollar bill that was not visually saturated with
ugliness. A counterfeiter with aesthetic sensibilities must not only
sweat blood but weep tears over the job of imitating one. But in the
sadly perverted taste of that epoch there was a kind of innocence:
standards were still respected, and proficiency, though overworked
and misdirected, was recognized and not condemned.
Today when I look about in the bookstore, and more especially on
the newsstands, or open the pages of most of the magazines with
the biggest circulations, I want to do what the little boy did in the
story which was a favorite of my friend, the late Hal Marchbanks.
The little boy had been to his first party, and when he arrived home,
his mother said: "Did mama's little boy have a nice time at the
party?" "Yep," he replied. "What did mama's little boy do at the
party?" "I thow'd up."
Against this steady decline in both taste and workmanship, your fifty
books selection and exhibit each year has been a noble effort, and in
this country, almost the only concerted one of consequence to
uphold some standards. You have inspired both publishers and
printers to earnest endeavor to improve their products with
frequently admirable results. But these are only fifty books out of
how many other books and other printed things. Without this good
work of yours, one wonders if any standards at all would survive the
flood of cheap and easy mechanization, careless workmanship and
bad taste. Not that there is anything wrong with machines. The first
hand press, it should be remembered by its sentimental admirers,
was also a machine. We have not learned to use the machines at
their best, but accepted them like fruits in the Garden of Eden, and
thought of nothing but how much we could get out of them in speed
and quantity and profit. Because we can do with them easily what
formerly demanded time and pains to do at all, we have too easily
assumed that they delivered us from the need of any time or pains.
Before I go any farther on or off the track with these random
remarks, I should like it to be understood that I am addressing them
particularly to any students and beginners in the graphic arts that
may be present, rather than to those who are arrived. I am a
student and still a beginner myself, and so my interest and my heart
are naturally with my own kindred. I speak as an old beginner to
younger ones. I am at a great disadvantage with regard to the
number of years I have left in which to get started, and if I have any
advantage at all, it is only in experience with the bewilderments and
illusions that clutter our common way in learning and trying to
practice one or more of the graphic arts. The confusions and
distraction of this day make the path of the student and beginner
rough and tortuous. Having travelled it for more years than I like to
admit, when I look backward, I am astonished to discover the
number of twists and turns and pitfalls I might just as well have
spared myself.
Perhaps the most foolish of these was the fear of not being original
—what Romain Rolland calls "the fear of the already said." The
notion that I must do something new every day, or I would not be
creative—forgetting that God made the planets all the same shape
as far as we can see, and that the oak tree does not alter the form
of its leaves from year to year. There is no supposition so
pathetically misleading as that creative originality is within your own
volition—the notion that it can be acquired leads to deplorable
results. It distracts the mind and energies of the young student from
gaining needful technical competence—from learning his trade, and
in more mature stages tempts the would-be artist into vulgar
mannerisms and formulas which he will call his "style."
The idea that originality is essential to the successful practice of the
graphic arts is more prevalent today than it ever was in the days
when the graphic arts were practiced at their best. The current belief
that everyone must now be an inventor is too often interpreted to
mean that no one need any longer be a workman. Hand in hand
with this premeditated individualism goes, more often than not, a
curious irritation with standards of any kind. The conscious cultivator
of his own individuality will go to extravagant lengths to escape the
pains imposed by a standard.
But of all the perils that lie in wait for adolescent artists there is
none more seductive than the bewildering array of ologies and isms
that leer and beckon to him at every crossroad of his journey. Just
as isms and ologies have taken the place, in social and political life,
of right and wrong; so have they become the accepted terms of the
arts. In fact, nonsense is now so universally the language of art that
it is nearly hopeless to try to make oneself understood in any other.
Brood mare to all of these extravagancies—and I have lived to see
many of them come and go—is that one which achieves the super
absurdity of calling itself "modernism"; and none has been
expounded and exploited in more contradictory and antic ways. To
deliberately call oneself "modern" is no less ludicrous than
something an old Danish friend told me years ago about a line in
one of the books of a very prolific writer of historical romances in his
country. In a tale with a medieval setting this writer had one of his
knights in armour cry out to another: "We men of the middle ages
never take insults, etc."
Embraced with fanatic enthusiasm by many architects and designers
is the current quackery called "Functionalism." It, in common with its
many predecessors, offers a new gospel for the regeneration of our
aesthetic world by restricting all design to the function of its object
or its materials. Like the new religions and philosophies that have
paraded in and out of our social history for countless generations, it
purports to be an original concept. It has brought to us such
gladsome gifts as concrete boxes with holes in them for buildings,
chairs of bent pipe with no hind legs, glass fireplaces, beds of
cement blocks joined by structural steel, the queer agglomeration of
unsightly edifices we call the World's Fair and many other specimens
of stark and forbidding claptrap. Unless all signs are misleading me,
it is another mass vulgarity like the age of golden oak and mission
furniture, even now on its way to the junk pile or the attic, perhaps
to be someday rediscovered there and dragged out by future
generations in search of quaintness.
It seems to me, ladies and gentlemen, that all art was modern when
it was made, and still is if it is suitable to life as we now live it; and I
look in vain for any applied art worthy the name that was not also,
in some sense functional. From the buttresses of a gothic cathedral
to the gayest Chippendale chair one finds, upon analysis, a perfect
work of engineering perfectly adapted to its purpose. If this were
not so, these things would hardly have endured for so long a time.
So that common regard for function which has always been the basic
principle of first-rate design, assumes the impressive aspect of a
religion, with high priests and ritual, by the simple addition of an
"ism." As students and beginners in search of truth, we are today
being pushed and pulled about by no end of such bogus
preachments—familiar faces with false whiskers—old and common
principles dolled up with new names and often used to account for
incompetence and laziness.
And what is the meaning of this term "functionalism"? Must a design
be related to no functions except mechanical and material ones?
Might not the most fantastic and elaborate works of the geniuses of
the baroque and rococo styles have also been functional in that they
expressed the spirit and fitted perfectly the life they were intended
to serve?
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Computational Structural Biology Methods and Applications 1st Edition Torsten Schwede

  • 1. Computational Structural Biology Methods and Applications 1st Edition Torsten Schwede pdf download https://ebookfinal.com/download/computational-structural-biology- methods-and-applications-1st-edition-torsten-schwede/ Explore and download more ebooks or textbooks at ebookfinal.com
  • 2. We have selected some products that you may be interested in Click the link to download now or visit ebookfinal.com for more options!. Multilingual FrameNets in Computational Lexicography Methods and Applications 1st Edition Hans C. Boas https://ebookfinal.com/download/multilingual-framenets-in- computational-lexicography-methods-and-applications-1st-edition-hans- c-boas/ Handbook of Research on Computational and Systems Biology Interdisciplinary Applications 1st Edition Limin Angela Liu https://ebookfinal.com/download/handbook-of-research-on-computational- and-systems-biology-interdisciplinary-applications-1st-edition-limin- angela-liu/ Health Monitoring of Structural Materials and Components Methods with Applications 1st Edition Douglas Adams https://ebookfinal.com/download/health-monitoring-of-structural- materials-and-components-methods-with-applications-1st-edition- douglas-adams/ Computational Methods for Plasticity Theory and Applications 1st Edition E. A. De Souza Neto https://ebookfinal.com/download/computational-methods-for-plasticity- theory-and-applications-1st-edition-e-a-de-souza-neto/
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  • 5. Computational Structural Biology Methods and Applications 1st Edition Torsten Schwede Digital Instant Download Author(s): Torsten Schwede, Torsten Schwede, Manuel C. Peitsch ISBN(s): 9789812778772, 9812778772 Edition: 1 File Details: PDF, 62.93 MB Year: 2008 Language: english
  • 8. 2nd Reading b587_FM.qxd 1/21/2008 4:15 PM Page ii This page intentionally left blank This page intentionally left blank
  • 9. World Scientific 6659tp.indd 2 1/31/08 7:43:09 PM
  • 10. Library of Congress Cataloging-in-Publication Data Computational structural biology : methods and applications / editors, Torsten Schwede, Manuel C. Peitsch. p. ; cm. Includes bibliographical references and index. ISBN-13: 978-981-277-877-2 (hardcover : alk. paper) ISBN-10: 981-277-877-2 (hardcover : alk. paper) 1. Proteins--Structure--Computer simulation. 2. Protein folding--Computer simulation. 3.Proteins--Structure--Mathematical models. 4. Protein folding--Mathematical models. 5. Computational biology. I. Schwede, Torsten. II. Peitsch, Manuel C. [DNLM: 1. Computational Biology--methods. 2. Protein Conformation. 3. Drug Design. 4. Nucleic Acid Conformation. 5. Protein Folding. 6. RNA. QU 26.5 C7385 2008] QP551.C714 2008 572'.6330285--dc22 2008001880 British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library. Typeset by Stallion Press Email: enquiries@stallionpress.com Printed in Singapore. Published by World Scientific Publishing Co. Pte. Ltd. 5 Toh Tuck Link, Singapore 596224 USA office: 27 Warren Street, Suite 401-402, Hackensack, NJ 07601 UK office: 57 Shelton Street, Covent Garden, London WC2H 9HE The cover illustration “Distortions” was created by Ansgar Philippsen, using DINO (www.dino3d.org) and POVray (www.povray.org). Distortions The act of visualization aims to reflect the data into a tangible representation, yet,withinitscontextualizedlayersofinterpretation,adistortionoftheoriginal state appears to be an almost unavoidable consequence. Copyright © 2008 by World Scientific Publishing Co. Pte. Ltd. All rights reserved. This book, or parts thereof, may not be reproduced in any form or by any means, electronic or mechanical, including photocopying, recording or any information storage and retrieval system now known or to be invented, without written permission from the Publisher. For photocopying of material in this volume, please pay a copying fee through the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, USA. In this case permission to photocopy is not required from the publisher. SC - Computational Structural Biology.pmd 7/23/2008, 7:02 PM 1
  • 11. Preface Computational structural biology aims primarily at establishing sequence-structure-function relationships for biological molecules using in silico techniques. This discipline emerged about 40 years ago (Levitt M. (2001). Nature Struct Biol 8:392–393) and has made much progress in the past decade. The purpose of this book is to pro- vide an overview of the progress in the field and to articulate some of the key challenges for the coming years. By no means could we cover the field comprehensively in just one book, and we thus focused on the structure and function of proteins and RNAs. The advent of large genome sequencing reinforced the observa- tion that structural information is needed to understand the detailed function and mechanism of biological molecules such as enzyme reac- tions and molecular recognition events. Furthermore, structures are obviously key to the design of molecules with new or improved func- tions. In this context, computational structural biology emerged as a discipline to develop computational tools to analyze and predict molecular structures and simulate their dynamical behavior. These theoretical approaches provide valuable insights into the detailed basis of molecular function and enable the effective design of experimental approaches to functional genomics. Major research topics include protein and RNA structure prediction, protein folding, protein and RNA dynamics with emphasis on large complexes and assemblies, molecular recognition, drug discovery and protein engineering. A key motivation for putting together this book came from our own experience, as 15 years ago we established the Swiss-Model, the first Web-based server for protein structure modeling. One major driver behind our vision was to mask much of the complexity associ- ated with protein modeling behind a simple interface, thereby pro- viding the scientific community with the possibility to gain insights v 2nd Reading b587_FM.qxd 1/21/2008 4:15 PM Page v
  • 12. into the 3D structures of proteins of interest, without the need to learn and purchase complex and expensive software. There are prob- ably three major factors contributing to the success of the Swiss- Model. First, the server is easy to use, as the Web-interface removes most of the complexity normally associated with protein modeling. Second, DeepView (also known as the Swiss-PdbViewer), which is available for most relevant computer platforms, has many powerful and easy-to-use features developed by modelers for modelers. Third, the uninterrupted operations for 15 years has allowed us to develop a robust and stable system. Today, well over 60,000 users build in excess of 400,000 models every single year and can access over a mil- lion pre-computed models available in the Swiss-Model Repository. Our objective is to continuously improve the performance of the server and the quality of the models it generates. We are particularly thankful to Nicolas Guex for his many crucial contributions to the development efforts of the Swiss-Model and the DeepView and to Gale Rhodes of the University of Southern Maine for coordinating the active DeepView user community. We also thank Alexander Diemand, Konstatin Arnold, Jürgen Kopp and Lorenza Bordoli for their many contributions to the development and opera- tions for the modeling platform. Furthermore, we are deeply indebted to Jake V. Maizel Jr, Timothy N.C. Wells, Jonathan C.K. Knowles, and Allan Baxter who have provided the necessary environ- ment and resources during the various phases of this project. Finally, we thank Stanley K. Burt, Robert W. Lebherz III, Karol Miaskiewicz and Jack R. Collins of the Advanced Biomedical Computing Center at the National Cancer Institute in Frederick Maryland for their sup- port in operating the US mirror of the Swiss-Model server. We grate- fully acknowledge the financial support by GlaxoSmithKline, Novartis, the Swiss National Science Foundation, the Biozentrum of the University of Basel and the Swiss Institute of Bioinformatics. T. Schwede and M.C. Peitsch vi Computational Structural Biology 2nd Reading b587_FM.qxd 1/21/2008 4:15 PM Page vi
  • 13. vii 2nd Reading Contents Preface v Section I STRUCTURE PREDICTION 1 AND ASSESSMENT METHODS Chapter 1 Protein Structure Modeling 3 T. Schwede, A. Sali, N. Eswar and M. C. Peitsch Chapter 2 Protein Fold Recognition and Threading 37 L. J. McGuffin Chapter 3 Scoring Functions for Protein Structure 61 Prediction Francisco Melo and Ernest Feytmans Chapter 4 Assessment of Protein Structure Predictions 89 E. Capriotti and M. A. Marti-Renom Chapter 5 The Biological Applications of Protein Models 111 A. Tramontano Section II FROM STRUCTURE TO FUNCTION 129 TO DESIGN Chapter 6 Evolution of Protein Folds 131 A. N. Lupas and K. K. Koretke b587_FM.qxd 1/21/2008 4:15 PM Page vii
  • 14. Chapter 7 Classification of Protein Structures 153 A. Cuff, O. Redfern and C. Orengo Chapter 8 Methods to Characterize the Structure 189 of Enzyme Binding Sites A. Kahraman and J. M. Thornton Chapter 9 Atomistic Simulations of Reactions 223 and Transition States M. Meuwly Chapter 10 Functional Motions in Biomolecules: 253 Insights from Computational Studies at Multiple Scales A. W. van Wynsberghe, L. Ma, X. Chen and Q. Cui Chapter 11 Protein-Protein Interactions 299 and Aggregation Processes R. I. Dima Chapter 12 Modeling and Simulation of Ion Channels 325 S. Bernèche and B. Roux Chapter 13 Milestones in Molecular Dynamics Simulations 363 of RNA Systems Y. Hashem, E. Westhof and P. Auffinger Chapter 14 Computational Protein Design 401 J. G. Saven Chapter 15 Prediction and Identification of B Cell 425 Epitopes Using Protein Sequence and Structure Information P. Andersen, D. Mkhailov and O. Lund viii Computational Structural Biology 2nd Reading b587_FM.qxd 1/21/2008 4:15 PM Page viii
  • 15. Chapter 16 Computational Antibody Engineering 445 T. K. Nevanen, N. Munck and U. Lamminmäki Section III DRUG DISCOVERY AND 467 PHARMACOLOGY Chapter 17 Small Molecule Docking 469 R. A. Friesner, M. Repasky and R. Farid Chapter 18 Structure-based Pharmacophores and Screening 501 R. Lewis and R. G. Karki Chapter 19 Molecular Dynamics-based Free 513 Energy Simulations M. A. Cuendet, V. Zoete and O. Michielin Chapter 20 Structure-based Computational Pharmacology 549 and Toxicology Angelo Vedani and Martin Smiesko Chapter 21 Structure-based Computational Approaches 573 to Drug Metabolism M. A. Lill Section IV NEW FRONTIERS IN EXPERIMENTAL 599 METHODS Chapter 22 New Frontiers in X-ray Crystallography 601 C. U. Stirnimann and M. G. Grütter Chapter 23 New Frontiers in High-Resolution 623 Electron Microscopy A. Engel Contents ix 2nd Reading b587_FM.qxd 1/21/2008 4:15 PM Page ix
  • 16. Chapter 24 New Frontiers in Characterizing Structure 655 and Dynamics by NMR M. Nilges, P. Markwick, T. Malliavin, W. Rieping and M. Habeck Section V SELECTED TOPICS 681 Chapter 25 Docking for Neglected Diseases 683 as Community Efforts M. Podvinec, T. Schwede and M. C. Peitsch Chapter 26 Protein Structure Databases 705 D. Dimitropoulos, M. John, E. Krissinel, R. Newman and G. J. Swaminathan Chapter 27 Molecular Graphics in Structural Biology 729 A. M. Lesk, H. J. Bernstein and F. C. Bernstein Index 771 x Computational Structural Biology 2nd Reading b587_FM.qxd 1/21/2008 4:15 PM Page x
  • 17. Section I Structure Prediction and Assessment Methods FA1 b587_Chapter-01.qxd 1/21/2008 2:44 PM Page 1
  • 18. FA1 b587_Chapter-01.qxd 1/21/2008 2:44 PM Page 2 This page intentionally left blank This page intentionally left blank
  • 19. 3 FA1 Chapter 1 Protein Structure Modeling T. Schwede*,† , A. Sali‡ , N. Eswar‡ and M. C. Peitsch§ 1.1 Introduction Knowledge of the three-dimensional (3D) structures of proteins pro- vides invaluable insights into the molecular basis of their functions. Furthermore, the design of experiments aimed at understanding molecular mechanisms — such as site-directed mutagenesis, mapping of disease-related mutations, and the structure-based design of spe- cific inhibitors — are greatly facilitated by the detailed knowledge of the spatial arrangement of key amino acid residues within the overall 3D structure. While great progress has been made in structure deter- mination using experimental methods, such as X-ray crystallography (Chapter 22), high-resolution electron microscopy (Chapter 23) and *Corresponding author. † Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingel- bergstrasse 50/70, 4056 Basel, Switzerland. E-mail: torsten.schwede@unibas.ch. ‡ Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, Byers Hall at Mission Bay, Suite 503B, 1700 4th Street, San Francisco, CA 94158-2330, USA. § Novartis Institutes of BioMedical Research, Basel Klybeckstrasse 141, 4057 Basel, Switzerland. b587_Chapter-01.qxd 1/21/2008 2:44 PM Page 3
  • 20. nuclear magnetic resonance (NMR) spectroscopy (Chapter 24), these approaches are generally still expensive, time consuming, and not always applicable. Currently, less than 50 000 experimental pro- tein structures have been released by the Protein Data Bank PDB1 (Table 1.1), while another 3500 have been deposited but are still awaiting release. These structures correspond to approximately 17 000 different proteins (sharing less than 90% sequence identity among one another). Nevertheless, the number of structurally char- acterized proteins is small compared to the 300 000 annotated and curated protein sequences in the Swiss-Prot section of the UniProtKB2 (http://www.expasy.org/sprot/). This number is even smaller when compared to the 5.2 million known protein sequences in the complete UniProtKB (October 2007). Even after removal of the highly redundant sequences from this database (above), the remaining 3.3 million sequences exceed the number of known 3D structures by more than two orders of magnitude. Thus, no experi- mental structure is available for the vast majority of protein sequences. This gap has widened over the last decade, despite the high-throughput X-ray crystallography pipelines developed for struc- tural genomics.3–5 Therefore, the gap in structural knowledge must be bridged by computation. Computational methods for predicting the 3D structures of pro- teins enjoy a high degree of interest and are the focus of many 4 Computational Structural Biology FA1 Table 1.1. Current PDB Holdings (October 2007)a Molecule Type Proteins Nucleic Protein/NA Acids Complexes Other Total Experimental X-ray 36847 991 1709 24 39571 Method NMR 5929 788 134 7 6858 EM 106 11 40 0 157 Other 83 4 4 2 93 Total 42965 1794 1887 33 46679 a The content of the table was obtained from http://www.pdb.org (1). EM: electron microscopy. b587_Chapter-01.qxd 1/21/2008 2:44 PM Page 4
  • 21. research and service development efforts. The prediction of the 3D structure of a protein from its amino acid sequence remains a funda- mental scientific problem and it is often considered as one of the grand challenges in computational biology and chemistry. Broadly, four different types of approaches are commonly in use. The first and most accurate approach is “comparative” or “homology” modeling that uses experimentally elucidated structures of related protein fam- ily members as templates to model the structure of the protein of interest (the “target”). These methods can only be employed when a detectable template of known structure is available. Second, fold recognition and threading methods are used to model proteins that have low or statistically insignificant sequence similarity to proteins of known structure (Chapter 2). Third, de novo (or ab initio) methods aim to predict the structure of a protein purely from its primary sequence, using principles of physics that govern protein folding and/or using information derived from known structures but without relying on any evolutionary relationship to known folds. Finally, a fourth group of methods, recently receiving a lot of attention, is the “integrative” or “hybrid” methods that combine information from a varied set of computational and experimental sources, including all those listed above. 1.2 Modeling Methods 1.2.1 Comparative Protein Structure Modeling Techniques Template-based protein modeling techniques (aka “homology model- ing” or “comparative modeling”) exploit the evolutionary relationship between a target protein and templates with known experimental structures, based on the observation that evolutionarily related sequences generally have similar 3D structures. Most comparative modeling procedures consist of several consecutive steps, which can be repeated iteratively until a satisfactory model is obtained: 1) identifica- tion of suitable template structures related to the target protein and the alignment of the target and template(s) sequences; 2) modeling of Protein Structure Modeling 5 FA1 b587_Chapter-01.qxd 1/21/2008 2:44 PM Page 5
  • 22. the structurally conserved regions and the prediction of structurally variable regions; 3) refinement of the initial model; and 4) evaluation of the resulting model(s). 1.2.1.1 Identification of modeling templates and sequence alignments Identifying suitable template structures and calculating an accurate alignment of their sequences with that of the target are the key first steps of the comparative modeling process. The sequence identity of the target-template alignment is the most commonly used metric to quantify the similarity between the target and template(s) and is also a good predictor of the quality of the resulting model. It is thus cru- cial to consider the target-template sequence identity level when selecting template structures (Sections 1.2.2, 1.6 and Chapter 5), as this will have a critical impact on the quality of the resulting model and hence, its potential applications. The overall accuracy of models calculated from alignments with sequence identities of 40% or higher is almost always good (i.e. deviate by less than 2Å RMSD from the experimentally determined structure) (Section 1.2.2). As the target– template sequence identity falls below 30–40%, models that deviate significantly from the average accuracy are frequent (i.e. deviate by more than 2Å RMSD from an experimentally-determined structure). Alignment errors also tend to rapidly increase in this regime and become the most frequent cause of large errors in comparative mod- els even when the correct template is chosen. Moreover, models based on alignments with such low sequence identities may have an entirely incorrect fold.6 While identifying and aligning sequences with similarities above 40% is relatively straightforward, more sensitive methods are needed for the lower levels of evolutionary relatedness between sequences. In recent years, significant progress has been made in the develop- ment of sensitive methods for sequence homology detection and alignment based on iterative profile searches, e.g. PSI-Blast,7 Hidden Markov Models, e.g. SAM,8 HMMER,9 or profile-profile alignment such as FFAS03,10 profile.scan,11 and HHsearch.12 Furthermore, in 6 Computational Structural Biology FA1 b587_Chapter-01.qxd 1/21/2008 2:44 PM Page 6
  • 23. the absence of a detectable sequence similarity, fold recognition and threading methods can be used to identify proteins with known structures, that share a common fold with the target sequence (Chapter 2). 1.2.1.2 Generating all-atom models Comparative protein structure modeling yields an all-atom model of a protein, based on its alignment to one or more related template structures. Over the years, two commonly used approaches for model building have emerged and can be described as follows: the first is a rigid fragment assembly approach, in which an initial model is con- structed from structurally conserved core regions of the template and from structural fragments obtained from either aligned or unrelated structures.13,14 The initial model is then subjected to an optimization procedure to refine its geometry and stereochemistry (Section 1.2.1.3). The second approach relies on a single optimization strategy that attempts to maximize the satisfaction of spatial restraints obtained from the target-template alignment, known protein structures, and molecular mechanics force-fields.15 Such an approach may not require a separate refinement step. However, most model building proce- dures are usually followed by the application of specialized protocols to enhance the accuracy of the non-conserved regions of the align- ment such as loops16,17 and/or side chains.18,19 1.2.1.3 Model refinement Once an atomic model has been obtained, it can potentially be refined to idealize bond geometry and to remove unfavorable contacts that may have been introduced by the initial modeling process. The refine- ment will generally begin with an energy minimization step using one of the molecular mechanics force fields.20,21 For further refinement, techniques such as molecular dynamics as well as Monte Carlo and genetic algorithm-based sampling methods22–24 can be applied. For instance, in certain cases molecular dynamics has been reported to yield some improvement of side chain contacts and rotamer states.25 Protein Structure Modeling 7 FA1 b587_Chapter-01.qxd 1/21/2008 2:44 PM Page 7
  • 24. Monte Carlo sampling with focus on regions most likely to contain errors, while allowing the whole structure to relax in a physically real- istic all-atom force field, can significantly improve the accuracy of models in terms of both the backbone conformations and the place- ment of core side chains.26 Nevertheless, limitations still exist in sam- pling as well as force field accuracy. 1.2.1.4 Model evaluation Model evaluation aims to recognize the various problems that might have occurred during the modeling process. Furthermore, estimating the overall geometrical accuracy of the individual regions of the model is an essential task of model evaluation. There are two kinds of evaluation schemes that are commonly employed. The first is “fold- assessment” that seeks to ensure the calculated models possess the correct fold and helps in detecting errors in template selection, fold recognition, and target-template alignment.6,27–29 The second class of methods seeks to identify the model that is closest to the native struc- ture out of a number of alternative models.30–37 A combination of such assessments is usually employed to select the most accurate model from amongst a set of alternative models, generated based on different templates and/or alignments. In general, addressing these different types of assessment requires specialized scoring systems and classifiers (Chapters 3 and 4). 1.2.2 Accuracy and Limitations of Comparative Protein Structure Modeling Comparative protein structure modeling relies on the evolutionary relationship between the target and template proteins. Consequently, the application of this approach is limited by 1) the availability of suitable template structures; 2) the ability of alignment methods to calculate an accurate alignment between the target and template sequences, even when the relationship between them is remote; and 3) the structural and functional divergence between the target and the template.38 8 Computational Structural Biology FA1 b587_Chapter-01.qxd 1/21/2008 2:44 PM Page 8
  • 25. The percentage of sequence identity between target and template correlates with model accuracy and often allows for a good first esti- mate of the model quality. As a rule of thumb, comparative models based on more than 50% sequence identity to their templates can be considered as “high accuracy models” and tend to have about 1 Å root mean square deviation (RMSD)38 for the main-chain atoms, which is comparable to the accuracy of a medium-resolution NMR- derived structure or a low-resolution X-ray structure.5,39 Inaccuracies are mainly found in the packing of side chains and loop regions. Comparative models based on 30 to 50% sequence identity can be considered “medium accuracy models”, where the most frequent errors include side-chain packing errors, slight distortions of the pro- tein core, inaccurate loop modeling, and sporadic alignment mistakes. Since alignment errors increase rapidly below 30% sequence identity and become the most substantial origin of errors in comparative mod- els, comparative models based on less than 30% sequence identity are considered “low accuracy models”. 1.2.2.1 Template availability and structural diversity It has been observed that a very small number of different folds account for the majority of known structures,40 and a recent study has argued that most sequences could already be modeled using known folds (or fragments of known folds) as templates.41 Thus, for the majority of target protein domains, a structure with a similar fold would be available within the Protein Data Bank (PDB). However, models based on alignments with low sequence identity often pro- vide accurate information only about the fold of the protein. As stated above, the accuracy of homology models decreases rapidly when the sequence identity between the target and template drops below 30%, mainly due to alignment errors and our inability to model structural differences between the target and the template. While the overall fold of proteins is often well conserved even at undetectable levels of sequence similarity, protein function — such as enzyme function and specificity — shows much higher variability,42,43 even at high levels of sequence identity (above 50%). New methods Protein Structure Modeling 9 FA1 b587_Chapter-01.qxd 1/21/2008 2:44 PM Page 9
  • 26. Discovering Diverse Content Through Random Scribd Documents
  • 29. Additional proofs of the Cleland ornaments were sent immediately to Mr. Rogers in London. With them he made eight designs, cutting the proofs and pasting the ornaments to show the desired effect. This tree, for instance, was used on the title page of the Barnacles insert: This was printed from a line engraving made direct from Mr. Rogers' paste-up, and used "as is" to show how accurately his layouts for this type of work reach the composing-room. A month later, in May 1931, Mr. Rogers returned his layouts with this note: "... I have only just been able to complete the designs I had begun.... One or two other combinations occurred to me, which I have also put in—but we could go on endlessly, almost, when once started on this kind of thing.... I would have built up the designs with impressions from sections of a slug, had you sent an inch or two of each unit; but it is perhaps better, though slower, to cut and paste proofs, as each cutting is a guide to the compositor as to how and where trimming or beveling the ornaments are necessary. But only a few such trimmings are required, and all the bevelings are at 45 degrees—as is the diagonal composition of the oak tree heads. "If at all possible I would like to have a chance to revise proofs of these, before they are actually printed—but if that isn't feasible, then I must rely on the compositors getting the closest possible approximation to my pasted-up designs. As close setting as possible is the secret of most work of this kind. The various parts must hang
  • 30. together well—though I do not mind a slight indication at the joints that they are made of individual pieces of type. I once had an over- zealous electrotyper fill up all the joints with solder—and ruined the appearance of the design—it looked like a drawn one." It wasn't possible to show Mr. Rogers what had been done with his layouts for the insert in Barnacles, which was essentially a surprise book distributed as a keepsake at a dinner in his honor. The "fighting cocks," to cite one instance, were originally suggested by B.R. to be used to dress a page folio at the bottom of the page; in the insert they were raised to the top of the page and printed with his initials. Other slight adaptations of similar character were taken in that piece of printing. "Typographic whimsy," wrote Carl Purington Rollins in B.R.— America's Typographic Playboy, in 1927, "is a pretty difficult achievement. The compositor at the case is too much concerned with the practical minutiæ of his craft to have much time for such trivialities, and the man who designs printing at a draughting board is apt to find his humor, if he attempts it in type, limping like a thrice-told jest. Mr. Rogers has had the advantage of enough familiarity with type to know what can be done, and he has been able at times to work with compositors who take a large and robust view of their calling." That "whimsy" Mr. Rollins had reference to lies in many of B.R.'s more ephemeral efforts, frequently reproduced. It is reflected to a measure, by The Symbol and the Saint page. But there is considerably more than whimsy in the type ornament designs by B.R. These have graced dozens of books of varying subjects ... and the marvel of it all is, to me, that the man never repeats himself—he swings off on a new tack ... adventurous, exploring, mastering new
  • 31. trails, scattering typographic inspiration for dozens of others, pointing up paths they previously never even suspected. Postscript, 1951: It is fitting to add a note concerning one of B.R.'s more distinguished recent projects, the great folio Bible designed for The World Publishing Company, which was four years in the making. The design of the World Bible employed decorative treatment for the bordered title page, the sixty-six book openings, initial letters and numerous tailpieces. "These, together with the type selected [a revised, special cutting of Goudy New-style], are intended to give a slightly oriental flavor to the volume," B.R. pointed out, "indicative of the Syriac and Hebrew sources of the text on which the King James translators based their classic version." In discussing the matter of ornaments in the Bible with the publishers, B.R. revealed his thinking concerning their use: "... Most of the Books will probably not begin at the top of the page and the use of ornaments are to me necessary to separate the end of the preceding book from the title of the following one.
  • 33. "The Bible has always been a book on which much decoration and illustrations have been lavished, and there is no reason in tradition why it should be treated solemnly in that respect. The very first edition (of which I have specimen sheets and a whole Bible printed from the same type and with the same decorations by the same printer, twenty-five years later, 1635) is just peppered with woodcut decorations and type ornaments. So we have a good precedent for a decorated treatment—if any were needed. You know the Bible is on the whole one of the most exciting texts in existence, and the modern 'practical' treatment of it as mainly a book of devotion is ignoble, to say the least...." Some of the typographic decoration and initials used in the Bible are included here. William Targ's detailed account, The Making of the Bruce Rogers World Bible, contains most of the decorative elements —initials, tailpieces and chapter initials—and reveals the intimate story of the progress of the book's production through the four years. It was published by World in 1949, in a limited edition of 1875 copies, 500 of which were for sale. COMPOSED IN CENTAUR AND ARRIGHI TYPES
  • 34. Book labels devised with typographic ornament by B. R. In the originals, a second color was used for each excepting the Reydel.
  • 35. SOME TENDENCIES IN MODERN TYPOGRAPHY Daniel Berkeley Updike From Some Aspects of Printing Old and New by D. B. Updike. Copyright 1941 by the author. Reprinted by permission of the Providence Public Library, Providence, Rhode Island. Not very long since I was asked by a printer to what extent he should accept or avoid modern trends in the design of types and books. I attempt here to answer that question. I have a friend, connected with one of the great companies supplying machines for type composition. Not long since he spoke to me in unflattering terms of the examples of typography shown at an exhibition of the products of the Bauhaus School, originally of Weimar and later of Munich. He protested against a practice there manifested of discarding capital letters and depending solely on those in the lower-case. I consoled him by showing him a French book, printed entirely in this style. This volume, entitled Typographie Économique, was published in Paris in 1837 and so far as it had any
  • 36. influence on printing, then or later, is as dead as Queen Anne. The author, the Count de Lasteyrie, who promoted this scheme, was one of a race of French scientists, of some intellectual and social importance—one of the daughters of Lafayette married into that family. In the eighteenth century no less a person than the German writer Grimm tried a similar typographical plan. In the Fairy Tales containing "Snow White and the Seven Dwarfs," later compiled by Jacob and Wilhelm Grimm, the practice was not continued. This supports the contention that many new and disturbing experiments, under the patronage of distinguished names, are merely survivals or revivals of ancient failures. Thus in the light of experience, there is in Bauhaus typography nothing for my acquaintance—or anybody else —to be excited about. Now Bauhaus typography is of the essence of modernism. That its position may be fairly stated I quote the following from a Bauhaus Year Book:—verbatim and (I may add) literatim: ["] why should we write and print with two alphabets? both a large and a small sign are not necessary to indicate one single sound. A = a we do not speak a capital A and a small a. we need only a single alphabet. it gives us practically the same result as the mixture of upper and lower-case letters, and at the same time is less of a burden on all who write—on school children, students, stenographers, professional and business men. it could be written much more quickly, especially on the type-writer, since the shift key would then become unnecessary, typewriting could therefore be more quickly mastered and typewriters would be cheaper because of simpler construction, printing would be cheaper, for fonts and type cases would be smaller, so that printing establishments would save space and their clients money. with these common sense
  • 37. economies in mind ... the bauhaus made a thorough alphabetical house-cleaning in all its printing, eliminating capitals from books, posters, catalogs, magazines, stationery and even calling cards. dropping capitals would be a less radical reform in english. indeed the use of capital letters occurs so infrequently in english in comparison with german that it is difficult to understand why such a superfluous alphabet should still be considered necessary.["] Now in German printing all nouns have capital letters. In the sentence "A Dog chases a Cat into a Barn," dog, cat, barn are all capitalized. No one can be blamed for wanting to be rid of so much capitalization. But when Germans purge anything the innocent invariably suffer with the guilty. Thus all capitals must go. While it may have overcome a difficulty felt in Germany, this imported missionary zeal corrects no difficulty in the printing of English prose or poetry. In some instances such a custom brings about surprising results. Suppose, for example, a newspaper says "the white house favors black and prefers even green to a dyed-in-the-wool red." To make the sentence intelligible would need the addition of a number of words—which would not be typographie économique! We need labour this point no further but leave these experiments to the advertising of Coty and Elizabeth Arden. Such effects have what is called attention value—like Neon signs—but I am not considering that kind of typography. I have, however, here traced the source of a current fashion of printing signs and advertisements without capital letters. I have been classed by my work as a conservative, but I am a liberal conservative or a conservative liberal—whichever you like or dislike. All I wish to conserve, either in traditionalism or modernism, is common sense. What little I have was gained by experience. I regard many typographic experiments with good will and many traditional viewpoints with tolerance. I agree wholeheartedly with neither. I remember—or try to do so—that every generation has in
  • 38. turn to be told that there was once a man named Caesar, who wrote a very dull book called the Commentaries, of which the first sentence is all that most people remember; that the makers of Baker's Chocolate did not invent the familiar picture of a chocolate girl, which was an eighteenth-century painting by Jean Etienne Liotard now in a Dresden picture gallery, and that William Blake did not write, but only illustrated, the Book of Job. We who have long known these things forget that people are born not knowing them. We should therefore look tenderly on many typographic experiments. To us elders they may seem akin to lighting a fire with kerosene or applying one's tongue to metal in zero temperatures, but it is by such unwise ventures that we outgrow them. And as I have spent a long life learning, and to most questions do not yet know the answers, I have no right to frown on more youthful and enterprising enquirers. Obviously some of the eccentricities of present-day typography are a natural reflection of that rather tortured world in which we find ourselves. If art, the drama, literature, and music reflect current trends of life it is natural that printing should in a measure do so. If we throw overboard old standards of conduct, we may far more readily throw over old standards of taste. When one casts a convention away as useless and outmoded, we often learn for the first time why it was there! It is urged that fuller expression of individuality, unhampered by rules, is development. It seems to me more accurate to say that through the experience of trying these experiments development comes—though not always of a kind expected. Such development ought never to stop until in the exact sense of the word we are "accomplished"—finished—which few live to be. The problem is to distinguish between a true development, and a false one. In judging either modernistic or retrospective typography, that is what must be decided. Do these developments—wise or otherwise, produce a well-made and readable book—in short a good book? "In the printing of books meant to be read," says an authority, "there is little room for 'bright' typography. Even dullness and
  • 39. monotony in the type-setting are far less vicious to a reader than typographical eccentricity or pleasantry. Cunning of this sort is desirable, even essential in the typography of propaganda, whether for commerce, politics, or religion because in such printing only the freshest survives inattention. But the typography of books, apart from the category of narrowly limited editions, requires an obedience to convention which is almost absolute—and with reason." It is the fashion, just now, to decry typographic conventions. Some conventions and traditions deserve to be decried and some have already been laughed out of existence. There are, however, good and bad conventions and traditions in printing, just as there are true and false developments, and the trick is to know which is which! Convention and particularly tradition are, generally, the crystallized result of past experiments, which experience has taught us are valuable. In some of the extreme modernistic typography a little more tradition might come in handy. The trouble with the modernist is that he seems afraid not to throw everything overboard and mistakes eccentricity for emancipation. Thus some books of today seem to be the arrangement of a perverse and self-conscious eccentricity. Such printing is often the work of eager, ambitious, and inexperienced men, and because they are young and God is good, one can afford to be patient; sure that they will, in the long run, outgrow the teething, mumps, and measles of typography. Their convalescence will possibly be hastened by meditating on the saying of Lord Falkland that "when it is not necessary to change, it is necessary not to change." No movement ever accomplishes all that its first promoters intended or hoped for; almost all movements make some lasting contributions to our common stock. Every new idea, every new invention brings along with its expected benefits unforeseen evils. Modernistic architecture is at present exciting because new and unusual; when more common it will become commonplace. When it becomes difficult to differentiate the exterior of a modernistic church from a warehouse, we may get very, very tired of it. Then a compensating reaction will set in and balance will be restored. The same thing is
  • 40. true of modernistic typography. At present, it shocks us into attention, but we get tired of being shocked, for we do not want printing to surprise but to soothe us. The modernist must remember, too, that "such a thing as an underivative work of art does not and cannot exist, and no great master in the arts has thought or asserted otherwise." We gladly admit that some modernistic formulas have had good results. In architecture, perhaps to some degree in typography, they have taught us to get rid of clutter and useless ornamentation. But neither the one nor the other leads anywhere—except to a dead end. The conservative, however, need not think that all truth is on his side. However much he tries to practise retrospective or "period" typography, consciously or unconsciously his work will show the influence of his time. Just as there is a popular idiom in speech which varies in each decade, so there is a current idiom in printing. All these idioms, literary and typographic, have not come to stay, but some become accepted terms. Under Theodore Roosevelt we suffered from the word "strenuous." President Harding inflicted the word "normalcy" on American speech. We now have "reactions," and "contacts." Clergymen "challenge" things, have "spiritual adventures," talk of "strategic positions" for their parish houses and aid parochial charities by "clarion calls," though if confronted with a "clarion" (if this instrument exists outside of sermons) they would be quite unable to blow it. All these catch-words and stock phrases are in the air. We suffer much the same thing in typography, about which there is also a new jargon which replaces the old clichés of my youth about rhythm, balance, and colour. Neither in speech nor printing can one make a clean sweep of the past nor help being of the present, no matter how hard one tries. I deplore violent attempts to make current printing accord with the spirit of the age. It always has, always will, and does now. Nor need the conservative sniff at typographic experimentation. To turn to another department of daily life, what would happen if no one had ever tried experiments with food? In the distant past there was the first human being who—as an experiment—ate an oyster,
  • 41. though perhaps first trying jelly-fish with less comfortable results. Others died of eating toadstools before people learned that they could survive on mushrooms. Almost all our vegetable food we owe to gastronomic adventurers. Thus the hide-bound conservative owes sustenance to the fruits, and vegetables, of experiment. To speak more seriously, both modernist and conservative should lay to heart what Benedetto Croce says in his Autobiography about "the impossibility of resting on the results of past thought" and the necessity of modesty in stating one's present position. "I see," he writes, "a new crop of problems springing up in a field from which I have but now reaped a harvest of solutions; I find myself calling in question the conclusions to which I have previously come; and these facts ... force me to recognize that truth will not let itself be tied fast.... They teach me modesty towards my present thoughts, which tomorrow will appear deficient and in need of correction, and indulgence towards myself of yesterday or the past, whose thoughts, however inadequate in the eyes of my present self, yet contained some real element of truth; and this modesty and indulgence pass into a sense of piety towards thinkers of the past, whom now I am careful not to blame, as once I blamed them, for their inability to do what no man, however great, can do ... to fix into eternity the fleeting moment." There is, to the reasonable mind, no real quarrel between modernism and traditionalism in printing, except in degree. Modernism must and does influence the conservative in spite of himself—if by modernism we mean a healthy awareness of the needs of the time in which we are living. Tradition must and does influence the modernist, if by tradition we mean patient and respectful appraisal of what that accumulation of yesterdays, which we call the past, has to teach. It is only by experience that we can effect a wise blend of the two. Then we produce books which, while representing the best practice of our time, will outlast it. The appraisal of their ultimate values we must leave to the future.
  • 42. "There is no past that we need long to return to," said Goethe, "there is only the eternally new which is formed out of enlarged elements of the past; and our real endeavor must always be towards new and better creation." COMPOSED IN BELL TYPES
  • 43. PETER BEILENSON The Amateur Printer: HIS PLEASURES AND HIS DUTIES From Graphic Forms: The Arts As Related to the Book. Copyright 1949 by Harvard University Press. Reprinted by permission of the publisher. Although the title of this piece is sufficiently long to be impressive and important-sounding, all I really want to write about is printing as fun. I am going to write about the amateur printer, and the amateur is the fellow who has fun. I do not wish to belittle the affection a professional printer may have for his work. He should love his work. But he can love it only in a different way: for after all he is essentially a businessman about it. His work, like that of any other businessman, is something he has to sit down to by nine in the morning and something he can't leave until five at night. It is something that involves landlords and labor unions, payrolls and tax inspectors, truckmen, office-boys, salesmen, compositors, pressman, bindery workers—and customers. He has to worry about payments, and depreciation, and publicity, and time sheets. The professional has to concern himself with all these things which are not printing at all, because he is in business and has to make money. His primary yardstick of success as a professional is: How much money did we make last year? Of course he has other minor
  • 44. yardsticks of success too: he may be successful because his presses turn out useful things like timetables, or gratifying things like corporation reports for the year, or beautiful things like four-color reproductions of Varga girls. To make these things well is a kind of fun; and insofar as the fun comes from the satisfaction in the thing itself rather than in the profit that derives from it, I'd like to call it amateur satisfaction. But essentially our professional printer—and permit me to limit myself to the professional book printer—is supposed to make money, not to have fun. And he makes money best, nowadays, if his plant is equipped with the efficient modern machinery which is designed for maximum production. Such machinery is a wonderful creation of man; it is thrilling to watch in action; and it gets results. But it has its disadvantages. Now that mechanization is becoming more and more complete in more and more places, we can begin to see clearly the greatest disadvantage of all: under such mechanization individual workers have lost pride and satisfaction in their work, because they have become mere replaceable units of less and less importance; whereas the machines they operate are more and more important, and have become the essential units. A generation ago the professional printer might have boasted of his skilled compositors, who could set type more expertly, or his skilled pressmen, who could make more careful overlays or match ink better than someone else's craftsmen. Today he boasts of his remote-control composing machines, his presses which come close to eliminating make-ready altogether, and his ink supplier's new gadget which matches colors scientifically. Today the most successful printer is the one who with the least possible dependence on man- power, can keep the most presses running fastest for the greatest number of hours per day and days per year. He is not the one with the most skilled craftsmen. In such a world, where the executive's function is to feed the machine and the workman's is to tend it, the human spirit begins to cry out for the fun in work which I have called the amateur
  • 45. satisfaction. It is true that today's shorter working hours—which the machine makes possible—permit people to have more outside fun; permit the manager to play more golf, and the workman to play more softball (or more pinball) in the late afternoon; it is true that more people now see more beer advertised on more television programs, and may even drink more of it, in the evenings. But managers and workmen alike turn so avidly to such kinds of fun because they no longer get fun out of their daily work. It is becoming harder and harder for people to equate work and happiness. Now I do not set myself up as a social reformer dedicated to the dream that all people should be happy in their work. Nor do I propose as a step to this end that we revert, smash the wonderful machines, and go back to the good old days when everyone really did work with his hands—usually from dawn to dark, six days a week. There was no pinball or television then, but still I do not wish to go back! Nor do I suggest that the solution is the promised thirty- hour week, with all the workmen driving their own Buicks home at two each afternoon, and taking out the wife and kiddies to Braves Field or the Gardner Museum. But I do suggest that some of you people who really love printing, but are too involved with the nine-to-five daily business of it to enjoy it much, should enrich your lives by becoming amateur printers in your spare time. You will have fun. I yield to no man in my boredom with vegetables and salads. I see green at every meal save breakfast. I have eaten enough stringbeans to stretch—if they were straightened out and laid end to end—from Fordhook Nurseries in Delaware to the city of Burbank, California. If you could see all the lettuce leaves I have consumed in my lifetime, piled leaf on leaf and dripping in their oils, their vinegar, their mayonnaise, and their roquefort dressings, you would be
  • 46. absolutely appalled. But, bored as I am with green things on the table—bored because despite their goodness they have been too plentiful and too easily come by—I am not bored on those occasions when, like Candide, I cultivate my garden, get my hands into the dirt, and smell God's good fragrance in the loam. To watch the power of living things like salad greens and stringbeans pushing their way out of the seed, up through the earth, reaching down for water and up for sunlight with an irresistible drive, is to realize afresh the power of life on this planet. It is a reinvigorating and religious experience. It is impossible to watch seeds grow into plants and flowers and fruit and still to believe cynically in a mere mechanistic explanation for such a life drive. To get back to the seed, the earth, and the root is to re-experience the fun and meaning of life. In the same way that I have become bored with salad, we have all become bored with words, printed words. We have seen too many of them, we have read too many of them, we have measured, or proofread, or edited, or sold, too many of them. We have forgotten their primal power, their irresistible living urge. We have forgotten that sincere authors have not put them down on paper because of two cents a word or 10 per cent of the retail gross—that they have been written (in the best cases) out of human necessity, human ebullience, human passion, human sympathy, or human understanding. The industrial book-printing world cannot ever think of words in that way. It must always think of them as areas of type 22 by 28 picas, as numbers of pages which do or do not make up a multiple of thirty-two, as units of sale at $3.00 less 40 per cent. To go back to nature and become an amateur printer in such an industrialized book world is like working in the garden when you are bored with salad. You really get back to the roots of words. If you are a genuine amateur printer, and set the type and print the pages yourself, you actually can share in the creative agonies and satisfactions of the author. For you put down his words, letter for letter in your type-stick, just as he did with his quill or his battered Remington. The best way on earth to appreciate an author and his
  • 47. creative spirit (or for that matter to realize more quickly the faults in him) is to pick him up letter by letter from a California case. An even more acid test is to distribute the type after printing him. In such a case you pick up half a dozen lines of type at once and work backwards, distributing the last word of the last line first. It is a revelation how the hollowness of an author can show up under this treatment. It is especially cruel to poets, for every word which is not really necessary, which is there just for padding or for a rhythm or a rhyme, becomes as noticeable as the well-known sore thumb. But the genuine, sincere author with a pure style stands up beautifully under such treatment, and has his reward in your pleasure at this discovery. After you have set your author's type you must make up his pages, choose his decorations or illustrations, and set his headings. You must decide whether to stretch him to twenty-four pages or condense him to sixteen. You must buy his paper, lock up his pages in your chase, make him ready, curse your press which is printing him, apply your ink to his words, and impress him for posterity. Perhaps you will thereafter fold him, sew him, and encase him in boards. In so doing, you become, to the extent of sixteen or twenty-four pages, in an edition of one hundred or three hundred copies, God. You have created something which did not exist before, and which would not have existed save for your thinking brain and tired back and dirty hands. True, you have not created Heaven and Earth, and you have undoubtedly worked at your creation for more than the original quota of six days. But anyway you have given the world something which was at first only words you loved, and is now a whole, real book, which you love all the more because it is your book, your child, your embodiment of those words. That is the fun and satisfaction of being an amateur. In our printing world there is no other satisfaction equal to it.
  • 48. Good old Ralph Waldo Emerson was mortally right when he wrote down his doctrine of Compensation. His doctrine of Compensation says that every pleasure carries some penalty, every gain some kind of loss. Every duty accepted gives you a satisfaction, and every satisfaction received involves you in a duty. Thus far I have written of the satisfaction of your being an amateur printer. Now I wish to write of your duty and obligation. The amateur book printer has a duty which, if he will accept it, will in the long run return to him the greatest satisfaction. This duty is to teach the professional, by example, about the outer cultural world, and to experiment for him in matters of printing style. Now this is directly contrary to what ninety out of one hundred current amateurs would seem to think, and I must therefore beg their ninety pardons if I disturb their habits of mind. Most amateurs either don't trouble their minds about problems of printing style at all, or else they fall too easily into the habit of working in the Colonial style, or Venetian style, or some other historical style, rather than in a contemporary one. Maybe they do so for psychological reasons. And maybe not. I am too set in my diction to learn the trick of talking in psychological terms. I would express their case like this: Amateurs who work in historical styles do so because they are romantics, romantics who turn away from the impersonal machine world of the present for a breath of the more human and glamorous-seeming past. I sympathize with such an instinct, and hold myself ready to defend any man who seeks to re- inject a human element into the printing craft. The trouble is, such amateurs think that because printing in the past was done by hand, and because there is something more satisfying and human about printing by hand, they must therefore work in an antique printing style and make Colonial and Venetian books in order to enjoy themselves. This is a false syllogism. I strongly recommend printing by hand to amateurs because it will give them greater satisfaction, not because it will make their books look like antiques. It is too easy to fabricate such antiques, and to do so will in the long
  • 49. run give you less enjoyment than making something which in style is original and new. As a matter of fact it is already too late to think in terms of revivals and reproductions. In printing, the revival habit started over a hundred years ago with Whittingham and Pickering, when they dusted off the forgotten Caslon types and the eighteenth-century style. It has been going on ever since, and reached a climax of understanding and skill in our century at the hands of Updike, Rogers, Rollins, Goudy, and others. This revivalism was a kind of search for humanism, and a kind of rebellion against commercialism. These men were not unique. In every generation since 1800, in every art and craft, every field of thought, the Industrial Revolution has prompted men to make the same search backward for satisfactions which the modern world did not seem to offer. Too many of our amateurs are still making the same search, although the Industrial Revolution is well over one hundred years old, all the necessary backward searching has been done, and all the historical styles have been reworked. Our predecessors have made it unnecessary for us to go through the process once again. We can see now that their work was an escape perhaps for them, but that it can never be a durable way of creative realization for us. From now on, we must join up with the forward-looking crowd who think they can build a new world. The book-printing industry has not been very forward-looking in matters of style. With the exception of a few printers and designers, book printers have been unhealthily backward. Therefore the time is ripe for amateur book-experimentalists to prod and teach them. The amateur can do it. He is, or should be, a man with interests in other fields of culture than his own. He is aware already of what has been done in painting and music, in fabrics and furniture design, in architecture too—most important of all. He must now help printing to develop its own new styles, equivalent to those in other fields. That he can do so is evidenced by the fact that in recent years the greatest strides
  • 50. forward have been taken not by the professionals but by people who in a sense are amateurs, but who have known how to apply modern ideas from other fields. The Bauhaus group first became notable, between the wars, by applying the functional theories of modern architecture to the printed page. The Black Sun Press and Harrison of Paris applied the ideas of Monroe Wheeler and others who were stimulated by modern painting. There may be similar publishing projects in this country today, but they are not yet influential. The most effective, most vocal, most lovable of contemporary American influences is that rugged individual Merle Armitage, whose ideas have been influential in shaping my own attitude. Such people all know that the world has changed; that it will never turn back again; and that it is up to us to catch on to the flying coattails of Today. I urge other amateurs to join the ranks of these apostles of change. It will be a great day for all of us when ninety out of one hundred are experimentalists, and not the other way around. Of course in urging amateurs to develop new styles, I am not recommending any easy hobby. It is simple, but dull, to copy an old style. It is hard, but exciting, to work out a new one. And while you are working at it, you must expect cynical observers to give your experiments the adjective "wacky"; you must expect certain curious kinds of people to praise your work for the wrong reasons; and you must expect alternating moods of conceit and frustration. The proofs you gloat over at night will become commonplace by dawn. Your wife may go back to her mother in rage and despair. You may need sleeping pills. You will make misjudgments about the intelligence of ordinary readers. You will make mistakes of taste. You will find it too easy to get an effect by means of shock, and you will forget that any book, even a twenty-first-century book, must be a coherent unit. And you will often, since there are no highway markers for the explorer, feel lonely and discouraged, and want to go back to the old familiar well- traveled roads again.
  • 51. But if you go through with it, or even if you just play with it sometimes as a hobby, you can have great fun. For it will put you out in the open, free to please yourself, with the boss and the customer left far behind. You can be subtle or bold, as you feel the urge, for you do not have to please the great common denominator, the common man. You can advance your own work by looking to other fields of creation, enjoying and profiting by the experiments going on in them. You can feel yourself a part of the whole forward- looking culture of your day, and not someone off in a little forgotten corner. And, if you do strike a vein with the glitter of real gold in it, you will become rich indeed. For you will have become a creator in a new sense; your duty done as an amateur will be compensated with a twenty-four-carat satisfaction. At such a moment of realization you will have earned the privilege to rest and feel content. As on a seventh day after six of creation, standing late at night with bloodshot eyes and inky fingers and aching back in a paper-littered room, you have become a creator. You have not merely escaped from the flattened monotony of the machine age—you have become one of the shapers of its future. More power to you in that work!
  • 52. T. M. CLELAND Harsh Words An address delivered at a meeting of The American Institute of Graphic Arts, in New York City, February 5th, 1940, on the occasion of the opening of the eighteenth annual exhibition of the Fifty Books of the Year. Copyright 1940 by T. M. Cleland. Reprinted by permission. Mr. Chairman and Members of The American Institute of Graphic Arts: The generosity of your invitation to me to speak on this important occasion leaves me a trifle bewildered. I am so accustomed to being told to keep my opinions to myself that being thus unexpectedly encouraged to express them gives me some cause to wonder if I have, or ever had, any opinions upon the graphic arts worth expressing. But since it is the theory of your Committee that I have, and it may never be anybody's theory again, and they have gone so far as to give me no instructions or suggestions as to the scope or the limitations of what I might say, it would seem as ungracious to decline such an exceptional offer as it would be to abuse it. So if I accept it as wholeheartedly as I believe it was given—if I take you at your word and say things that I have long wanted to hear somebody say—I hope it will not be thought an abuse of this kindly tendered privilege. I realize that, nominally at least, my subject must be that of printing and typography as exemplified by the selection of the fifty best
  • 53. books of the year which we are here to celebrate; and I suppose, by comparison to deplore the fifty thousand worst books which may be seen elsewhere. But by what may seem a very odd paradox, I don't quite know how to stick to this subject without wandering a good way off it. Or, perhaps I should say that I cannot approach it directly except by a very roundabout way. If I have a thesis for these remarks, I can only develop it in terms of a tree. This is because I do not believe that invention in the arts can be picked from empty space like objects in a prestidigitator's act. Fruits really grow on trees and trees have roots in the earth. The tree I have in mind is cultural civilization: one of its limbs is art and a branch of this we call the graphic arts, and a twig on this branch is printing and typography. I promise not to dig into the roots of this tree, but I may be found, monkey-wise, climbing all over it before I am through. I am at some disadvantage in that I do not belong to any organizations for the advancement of typography and the graphic arts—not even to this one—and I am ill-informed and out of touch with what is going on in these fields except by casual observation. But as members of this very useful organization, you are not engaged in printing or other graphic arts, I take it, solely for each other, but for the enjoyment and delectation of the world at large. So there is a partially compensating advantage in my being "at large" myself, and thus able to speak of present trends in the graphic arts as they appear from the outside, looking in. But this advantage may in turn be offset by the fact that I cannot honestly speak of what I see with much enthusiasm. I can bring you no message of hope or light of inspiration. Much as I am filled with admiration and respect for many individual talents and accomplishments that still contrive to exist, they seem to me to stand unhappily isolated in what I can't help viewing as artistic bankruptcy and cultural chaos. Among them are printers making beautiful books and other things about as well as these things have ever been made. But as to the general volume of printing, no one has asked me, to be sure, what I thought was the lowest point of
  • 54. artistic taste in the five hundred years of its existence which we are celebrating this year, but if anyone should ask me, I would be bound to say that we have reached that point just about now. Things may get worse, but it's hard to see how they can. To paraphrase a remark in the concluding chapter of Updike's classic work on printing types, it has taken printers and publishers five hundred years to find out how wretchedly books and other things can be made and still sell. I am not forgetting that there were some very benighted periods of taste in other centuries that would seem to refute this sweeping assertion. Perhaps it is worth noting here—and the fact is peculiarly ironical—that the design and style of official and governmental things—money, postage stamps, bonds and stock certificates—was created and solidified into a seemingly unalterable convention at that hitherto all time low point of the decorative arts in the mid- nineteenth century. So powerful is this convention that we would be suspicious of a ten dollar bill that was not visually saturated with ugliness. A counterfeiter with aesthetic sensibilities must not only sweat blood but weep tears over the job of imitating one. But in the sadly perverted taste of that epoch there was a kind of innocence: standards were still respected, and proficiency, though overworked and misdirected, was recognized and not condemned. Today when I look about in the bookstore, and more especially on the newsstands, or open the pages of most of the magazines with the biggest circulations, I want to do what the little boy did in the story which was a favorite of my friend, the late Hal Marchbanks. The little boy had been to his first party, and when he arrived home, his mother said: "Did mama's little boy have a nice time at the party?" "Yep," he replied. "What did mama's little boy do at the party?" "I thow'd up." Against this steady decline in both taste and workmanship, your fifty books selection and exhibit each year has been a noble effort, and in this country, almost the only concerted one of consequence to uphold some standards. You have inspired both publishers and
  • 55. printers to earnest endeavor to improve their products with frequently admirable results. But these are only fifty books out of how many other books and other printed things. Without this good work of yours, one wonders if any standards at all would survive the flood of cheap and easy mechanization, careless workmanship and bad taste. Not that there is anything wrong with machines. The first hand press, it should be remembered by its sentimental admirers, was also a machine. We have not learned to use the machines at their best, but accepted them like fruits in the Garden of Eden, and thought of nothing but how much we could get out of them in speed and quantity and profit. Because we can do with them easily what formerly demanded time and pains to do at all, we have too easily assumed that they delivered us from the need of any time or pains. Before I go any farther on or off the track with these random remarks, I should like it to be understood that I am addressing them particularly to any students and beginners in the graphic arts that may be present, rather than to those who are arrived. I am a student and still a beginner myself, and so my interest and my heart are naturally with my own kindred. I speak as an old beginner to younger ones. I am at a great disadvantage with regard to the number of years I have left in which to get started, and if I have any advantage at all, it is only in experience with the bewilderments and illusions that clutter our common way in learning and trying to practice one or more of the graphic arts. The confusions and distraction of this day make the path of the student and beginner rough and tortuous. Having travelled it for more years than I like to admit, when I look backward, I am astonished to discover the number of twists and turns and pitfalls I might just as well have spared myself. Perhaps the most foolish of these was the fear of not being original —what Romain Rolland calls "the fear of the already said." The notion that I must do something new every day, or I would not be creative—forgetting that God made the planets all the same shape as far as we can see, and that the oak tree does not alter the form of its leaves from year to year. There is no supposition so
  • 56. pathetically misleading as that creative originality is within your own volition—the notion that it can be acquired leads to deplorable results. It distracts the mind and energies of the young student from gaining needful technical competence—from learning his trade, and in more mature stages tempts the would-be artist into vulgar mannerisms and formulas which he will call his "style." The idea that originality is essential to the successful practice of the graphic arts is more prevalent today than it ever was in the days when the graphic arts were practiced at their best. The current belief that everyone must now be an inventor is too often interpreted to mean that no one need any longer be a workman. Hand in hand with this premeditated individualism goes, more often than not, a curious irritation with standards of any kind. The conscious cultivator of his own individuality will go to extravagant lengths to escape the pains imposed by a standard. But of all the perils that lie in wait for adolescent artists there is none more seductive than the bewildering array of ologies and isms that leer and beckon to him at every crossroad of his journey. Just as isms and ologies have taken the place, in social and political life, of right and wrong; so have they become the accepted terms of the arts. In fact, nonsense is now so universally the language of art that it is nearly hopeless to try to make oneself understood in any other. Brood mare to all of these extravagancies—and I have lived to see many of them come and go—is that one which achieves the super absurdity of calling itself "modernism"; and none has been expounded and exploited in more contradictory and antic ways. To deliberately call oneself "modern" is no less ludicrous than something an old Danish friend told me years ago about a line in one of the books of a very prolific writer of historical romances in his country. In a tale with a medieval setting this writer had one of his knights in armour cry out to another: "We men of the middle ages never take insults, etc." Embraced with fanatic enthusiasm by many architects and designers is the current quackery called "Functionalism." It, in common with its
  • 57. many predecessors, offers a new gospel for the regeneration of our aesthetic world by restricting all design to the function of its object or its materials. Like the new religions and philosophies that have paraded in and out of our social history for countless generations, it purports to be an original concept. It has brought to us such gladsome gifts as concrete boxes with holes in them for buildings, chairs of bent pipe with no hind legs, glass fireplaces, beds of cement blocks joined by structural steel, the queer agglomeration of unsightly edifices we call the World's Fair and many other specimens of stark and forbidding claptrap. Unless all signs are misleading me, it is another mass vulgarity like the age of golden oak and mission furniture, even now on its way to the junk pile or the attic, perhaps to be someday rediscovered there and dragged out by future generations in search of quaintness. It seems to me, ladies and gentlemen, that all art was modern when it was made, and still is if it is suitable to life as we now live it; and I look in vain for any applied art worthy the name that was not also, in some sense functional. From the buttresses of a gothic cathedral to the gayest Chippendale chair one finds, upon analysis, a perfect work of engineering perfectly adapted to its purpose. If this were not so, these things would hardly have endured for so long a time. So that common regard for function which has always been the basic principle of first-rate design, assumes the impressive aspect of a religion, with high priests and ritual, by the simple addition of an "ism." As students and beginners in search of truth, we are today being pushed and pulled about by no end of such bogus preachments—familiar faces with false whiskers—old and common principles dolled up with new names and often used to account for incompetence and laziness. And what is the meaning of this term "functionalism"? Must a design be related to no functions except mechanical and material ones? Might not the most fantastic and elaborate works of the geniuses of the baroque and rococo styles have also been functional in that they expressed the spirit and fitted perfectly the life they were intended to serve?
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