- This Gallery features animated (rotating) molecules in GIF images prepared by the
PDB2MGIF Server. Such images are easy to prepare, using the form on this server, and can be displayed on web pages or in PowerPoint presentations.
- Submitted by: Martz, Eric. (Entry 10).
- Co-authors: Ranzinger, René. Submitted by: the author. (Entry 16).
SYMMATION offers 2D and 3D illustration and animation services for the fields of medicine, science, education, museum exhibits and other health care and technology-based groups. We specialize in providing atomic resolution molecular illustrations and animations for publication, broadcast and multimedia
We are gearing up to deliver animations for ALL Protein Data Bank entries via a database system. Site visitors will be able to customize their animations and retrieve these once rendered and composited (all machine-driven).
Software titles we use are: 3D Studio MAX, softimage XSI, molscript, pymol and other in-house tools. We have an extensive feedback system with our clients, both commercial as well as 'non-profit'.
- Submitted by: the author. (Entry 15).
-
Images created with the
SPOCK molecular graphics software package, which can be publication quality. Software is for unix/linux/irix only. Free for non-profit use.
- Submitted by: Foley, Brian. (Entry 14).
- Dr. Arnold's Lab
studies reverse transcriptase (RT), which is an
essential component of the AIDS virus and the target of many of
the most widely used anti-AIDS drugs. Using the techniques of
X-ray crystallography, his team has solved the three-dimensional
structures of HIV-1 RT in complex with antiviral drugs and pieces
of the HIV genome. These studies have illuminated the working of
an intricate and fascinating biological machine in atom-by-atom
detail and have yielded numerous novel insights into polymerase
structure-function relationships, detailed mechanisms of drug
resistance, and structure-based design of RT inhibitors. Synthesis
of the information being developed has lead to the development of
inhibitors that show great promise as potential treatments for
AIDS.
Dr. Kalyan Das has created graphic images of the HIV-1 reverse transcriptase protein, alone and in complex with DNA:RNA heterodeplexes, antiretroviral drugs, and nucleotides. A movie of HIV-1 RT "breathing" as it elongates a DNA chain during the reverse transcriptase process is currently being created.
- Submitted by: Foley, Brian. (Entry 12).
- Our database includes hundreds of molecular-tagged images and tens of thousands of medical images. Fotosearch Stock Photography and Stock Footage helps you find the perfect photo or footage, fast! Our search engine features 2,000,000 royalty free photos, 40,000 stock footage clips, digital videos, vector clip art images, medical illustrations, and maps.
Comment added by Eric Martz: THIS IS A COMMERCIAL SITE, but searching for "dna" or "hiv", etc. does produce a lot of potentially useful images. However, you must pay for use of even the "royalty-free" images.- Submitted by: the author. (Entry 21).
- A gallery of images created with UCSF Chimera. There is also an Animation Gallery.
- Co-authors: Couch, Greg; Pettersen, Eric; Goddard, Tom; Greenblatt, Daniel; Meng, Elaine; Ferrin, Thomas. Submitted by: Meng, Elaine. (Entry 20).
The gOpenMol
freeware is the graphics interface to the OpenMol set of programs. gOpenMol
can also be used for the analysis and display of molecular dynamics
trajectories and the display of molecular orbitals, electron densities and
electrostatic potentials from programs like the GaussianXX, PC GAMESS and
Jaguar. The Gallery includes images representing
- root mean square fluctuation of the C(alpha) atoms as ellipsoids
- space inside which a water molecule moves during the simulation
- transparent Connolly surface. The same surface coloured according to the electrostatic potential.
- coloured according to the force acting on the atoms, with force vectors for water molecules (portion shown at left)
- Molecular orbital display. Wave function (orbitals) generated with the Gaussian94 program.
- Si-impurity As-vacancy defect complex in GaAs.
- isodensity surface of valence electrons in sodium clusters
- Rydberg States of Weakly Interacting Systems
- University of Houston Brownian Dynamics calculation on acetylcholine-esterase showing various display styles of the electrostatic potential.
- Solvation Structures in Liquid Mixtures
- Distrubutions of Counterions around DNA. Molecular Dynamics Simulations Results.
- Submitted by: Martz, Eric. (Entry 8).
- Galleries of images created with Roger Sayle's RasMol. Images by Roger Sayle and Eric Martz.
- Co-authors: Sayle, Roger. Submitted by: the author. (Entry 1).
- A gallery of images by non-RasMol/Chime software, with links to many other molecular galleries.
- Submitted by: the author. (Entry 2).
This illustrated page traces the use of physical models of proteins from the early Kendrew wire models at the dawn of protein crystallography, through Byron's Bender, molecular sculpture, and rapid prototype engineering.
Sculpture at the Smithsonian Institution. Image copyright © 2001, Byron H. Rubin, with permission.Coverage of computer representations starts in the 1960's (with movies from a computer in Cyrus Levinthal's group at MIT), and continues through electronic Richards' boxes, TAMS, Evans & Sutherland computers, Kinemages, RasMol and Chime.
- Co-authors: Francoeur, Eric. Submitted by: the author. (Entry 7).
-
Browsable short descriptions and links to over 70 PDB files. PDB ID codes are listed. Clicking a link displays the molecule in
Protein Explorer. The Atlas is divided into over a dozen sections, such as enzymes, soluble proteins, structural proteins, integral membrane proteins, DNA/RNA, proteins complexed to nucleic acids, whole virus capsids, anthrax toxins, immuno-molecules, carbohydrates, unusual tertiary/quaternary structures, and "magnificent molecular machines". Small screenshots decorate the Atlas. Nominations of molecules to include in the Atlas are welcome.
- Submitted by: the author. (Entry 9).
- Molecular Art of protein structures and molecular dynamic simulations. Exploring the beauty of protein structures using standard visualization programs such as Pymol and VMD.
- Submitted by: the author. (Entry 17).
Gallery of images for molecular structures created with BALLView. - Co-authors: Hildebrandt, A; Lenhof, H.P., Kohlbacher, O.. Submitted by: the author. (Entry 18).
- SWISS-3D-IMAGE is an image database which strives to provide high quality pictures of biological macromolecules with known
three-dimensional structure. The database contains mostly images of experimentally elucidated structures, but also provides views of well accepted theoretical
protein models.
The images are provided in several useful formats; both mono and stereo pictures are generally available. Images are searchable and annotated.
- Submitted by: Martz, Eric. (Entry 4).
- A gallery of images that utilize molecular visualization in the field of Medical Illustration.
The images employ Chime, RasMol, WebLab Viewer Lite, and a variety of graphics applications on the Macintosh.
- Submitted by: the author. (Entry 6).
- The IMB Jena Image Library of Biological Macromolecules is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and
analysis. It provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). In addition, basic information on the architecture of biopolymer
structures is available. The IMB Jena Image Library intends to fulfill both scientific and educational needs.
- Co-authors: Reichert, Jan. Submitted by: Martz, Eric. (Entry 3).
- All of the molecular graphics on this page were made with VMD via its "snapshot" feature, or through exported renderings to external ray tracers such as Tachyon, POV-Ray, Raster3D, and others. If you have an image you would like to contribute to the gallery, please email vmd@ks.uiuc.edu with instructions for downloading your image or send as an attachment. Providing us with a brief description of the image and an optional URL would allow us to make a link to to your web site and our visitors would be able learn more about your research. All images in our gallery are copyrighted by their respective authors. To make a reproduction any of the images you would need to contact the original authors for permission.
- Submitted by: Foley, Brian. (Entry 13).
Virusworld is collection of static images as well as MPEG, GIF and QuickTime movie of viruses. Viruses are listed by name in a pull-down menu and all existing images and animations, artistic or scientific, are automatically placed within a dynamically rendered web page.
The most recent addition are the images of the ICTV 8th report color plates, and the individual images that were assembled on the plates.
Most of the images can be used by students and professors to illustrate viruses in class. Permission to use is requested in any for-profit venture.
For each entry a link is given to both the PDB site and the new VIPER (VIrus Particle ExploreR) site where suitable PDB coordinates can be found or calulated.
Please note that some of the images are copyrighted by Academic Press or other authors and cannot be used without permission. However there are many images that can be used for academic endeavour without permission.
- Submitted by: the author. (Entry 19).
- DSMM is a Database of Simulated Molecular Motions. This database is designed to serve as a single searchable site for locating movies and animations from simulations of biomolecules. DSMM is accessible via a webserver at: http://projects.eml.org/mcm/database/dsmm.
Many molecular modeling and simulation studies have contributed to our understanding of biomolecular dynamics. Movies of trajectories from molecular simulations and animations consisting of concatenated snapshots of molecules provide a valuable means to visualize the results of such studies. They are insightful in the research context and a useful teaching aid in the classroom. Such movies often summarize the results of many CPU hours of simulation. However, they are rarely to be found in the final published results. Instead, many authors put their movies on their own web pages. This means that it is not easy to find out which movies are available, and searching for particular movies is a somewhat haphazard and unreliable process. Consequently, we decided to build a web-accessible database, DSMM, which would store information on molecular movies at a single location where they could be easily searched and located.
All movies collected in DSMM are results from simulations including molecular dynamics, Brownian dynamics, docking, energy minimization, NMR refinement and QM/MM calculations. Some of these simulations are run with the aim of obtaining a realistic picture of the dynamics of molecules as a function of time. In other cases, simulation techniques are used to derive specific information related to molecular function, such as low energy conformations or thermodynamic quantities. In the latter cases, movies can illuminate certain aspects of a molecule's function or how a particular simulation technique works, e.g. how a simulation-based ligand-docking technique converges on docked solutions. DSMM consequently contains movies of "molecular motions" that are all "simulated" but that may illustrate quite diverse aspects of molecular dynamics.
There are currently over 100 movies collected in DSMM. Authors are encouraged to enter their own movies into DSMM via the movie submission webpage.
- Co-authors: Finocchiaro, G, Wang, T., Hoffmann, R, Gonzalez, A.. Submitted by: the author. (Entry 11).