POLYVIEW-3D TutorialIntroductionGeneral notesPOLYVIEW-3D is a web-based tool for macromolecular structure visualization and analysis. In particular, it provides a wide array of options for automated structural and functional analysis of proteins and their complexes. This tutorial aims to describe and illustrate the available rendering options and annotation capabilities of POLYVIEW-3D. Server is available at http://polyview.cchmc.org/polyview3d.html. By integrating the web technology with state-of-the-art software for macromolecular visualization, POLYVIEW-3D enables versatile structural and functional annotations coupled with publication quality structure rendering. In addition to static pictures, high quality animated images for electronic resources such as PowerPoint or Web-sites can be easily generated with POLYVIEW-3D as well. In particular, POLYVIEW-3D server features the PyMol program for image rendering, providing detailed and high quality presentation of macromolecular structures, with an easy to use web-based interface. The service is platform independent and no plug-ins are required. The use of the server and its results are freely available for all users, as long as proper citations and acknowledgments are included (see below for POLYVIEW references). However, in the interest of better serving the community with limited computational resources, we reserve the right to limit the number of submissions (e.g., per day) from individual users. We would like to thank the authors of PyMol, RasMol, DSSP and other programs that are utilized by the server (see the list in the Summary section) for making them available to the community and graciously agreeing to incorporate them into a public domain server. We also gratefully acknowledge the support from NIH, University of Cincinnati College of Medicine and Cincinnati Children's Hospital Medical Center. Finally, we would like to point out that there are quite many visualization tools that are available on-line, often with complementary capabilities. One good resource to start exploring the field of macromolecular visualization is World Index of Molecular Visualization Resources. POLYVIEW-3D focuses on annotation and visualization of protein complexes. In order to automate complex annotation tasks, it is coupled with a number of protein analysis and prediction servers, including ConSurf, CASTp, SABLE, SPPIDER, SCORPPION, as well as our previous POLYVIEW web server for protein structure visualization. Therefore, we believe that POLYVIEW-3D may become an important resource for researches and educators in structural bioinformatics, protein science and related fields. Time permitting, we will make an effort to further improve the server. Feedback regarding bugs and annoying features, as well as suggestions for improvements are highly appreciated (please use link below to contact us). References and contact informationFor citation, please use the following references: Porollo A, Meller J: Versatile Annotation and Publication Quality Visualization of Protein Complexes Using POLYVIEW-3D, BMC Bioinformatics 2007, 8: 316. POLYVIEW-3D: http://polyview.cchmc.org/polyview3d.html Contact us and submit your feedback here. About this tutorialThis tutorial consists of several sections that describe distinct and functionally related groups of rendering and annotation options. In order to simplify the use of the tutorial a navigation menu with expandable items is included in the left hand panel, (please click on the respective entries to toggle submenu lists). As a general rule, each section contains a brief description of selected rendering and other options of interest, which are subsequently illustrated by examples of images generated with these options. In order to to lower the learning curve, these images are cross-linked with separate pages that contain larger versions of the images and the corresponding step-by-step instructions as to how to generate them using the server. Most of the examples are generated using the PyMol rendering program as it produces high quality images. As an alternative, RasMol-based rendering is also available. Both programs support most of the options provided by POLYVIEW-3D with a few differences: (1) RasMol does not fully support protein surface rendering; Therefore, this option, if chosen, is automatically replaced by spherical (CPK) representation; (2) The build of PyMol (v 0.99, rev 6), which is used by POLYVIEW-3D, has a problem rendering text labels in batch mode; Therefore, the option to assign labels to selected residues is available with the RasMol rendering only; (3) RasMol and PyMol use different coordinate systems to display macromolecules, leading to problems with the initial orientation required to achieve the same structure projection. However, one can use a Jmol-based utility to set up the initial orientation of the molecule to address the latter problem (see the section Initial orientation for details). All images generated by the server can be further improved using a script for rendering provided with the corresponding picture. Thus, one can use PyMol or RasMol installed locally to improve image quality if necessary. Scripts can also serve as examples of command syntax and functionalities of the respective visualization programs, providing further hints as to how to optimize the use of the server. POLYVIEW-3D provides a wide variety of options for both: molecular visualization and protein structure analysis. These different options and pertaining to them settings have been grouped into several distinct field sets that are displayed and activated in a context-dependent manner. For example, settings pertaining to animated images are only active when an animation (as opposed to a single slide) is requested, whereas settings pertaining to user provided tailored PDB files, e.g., with protein docking models in the CAPRI format, are only active when such a file is selected to be uploaded.
Currently, there are seven groups of settings:
(1) Source of structural data to
search and specify the file with 3D coordinates of a
macromolecular structure;
(2) Overall structure view to
set up the model number (if multiple) to render, the way
of presenting ligands and/or solvent, initial
structure orientation, and center of view.
(3) Chain coloring and rendering
settings to be applied to each chain;
(4) Residues highlighting
settings for highlighting particular residues of interest,
using both the color and rendering mode, e.g., spherical
representation for some residues vs. cartoon for
the rest of the chain;
(5) Advanced structure annotation
settings;
(6) Image settings for
defining general image parameters, such as
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