- Cross-indexing terms:
PyMol; PovRay; publication-quality image maker.
Comment by Eric Martz (emartz@microbio.umass.edu), October 2006: Not recommended for those wanting an easy, quick hi-resolution molecular view. I recommend Polyview-3D instead (below). I found AISMIG very slow and not easy to use. After spending about one hour with it, I failed to get any final hi-res image of the protein I submitted (1hho). The server simply returned me to the job submission page after a long delay.
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Authors:
Bohne-Lang, Andreas; Ranzinger, René.
Submitted by: Decatur, Wayne.
(Entry 14). Submitted on Oct 23, 2006. Last revised on Oct 23, 2006.
- Cross-indexing terms:
evolutionary conservation; functional regions; Jmol.
This server colors each amino acid in a protein chain according to its level of evolutionary conservation, thus helping to identify functional regions. Only a PDB code and a chain name need be supplied; the rest is automatic (although there are many options for advanced users). The process involves gathering similar sequences, creating a multiple sequence alignment, a phylogenetic tree, and calculating conservation levels, all done automatically.
The results can be viewed with FirstGlance in Jmol (Windows, Safari on OSX, Firefox on linux). Snapshots can be captured for pasting into Powerpoint (instructions are provided).
Rotating image at right is enolase (4ENL). Rotating multi-GIFs colored by ConSurf can be produced at PDB2MultiGIF (below) using RasMol coloring scripts generated by ConSurf.
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Authors:
Ben-Tal, Nir; Glaser, Fabian; Pupko, Tal; Landau, Meytal; Mayrose, Itay; Rosenberg, Yossi; Martz, Eric.
Submitted by: Martz, Eric.
(Entry 12). Submitted on Oct 21, 2006. Last revised on Oct 21, 2006.
- Cross-indexing terms:
movie maker; Pymol movie maker.
eMovie is a free tool that makes the creation of molecular movies both easy and intuitive via a breakthrough storyboard interface, similar in nature to what is used in the creation of traditional movies. eMovie is a plug-in for PyMOL, a powerful, open source, and multi-platform molecular graphics program. To download eMovie, visit the eMovie website at http://www.weizmann.ac.il/ISPC/eMovie.html.
Through eMovie, the user has the ability to construct an animation of any length out of building blocks like rotations, zooming, color changes, fading of selections, view changes, and even execution of specific PyMOL commands or scripts. Conformation changes and docking actions can be added as well (requires incentive version of PyMOL). Movies can be saved and loaded at a later time, and optionally exported as a ray-traced image sequences to be merged into a traditional movie file (e.g. .mov or .gif) using available external programs.
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Authors:
Hodis, Eran; Schreiber, Gideon; Rother, Kristian; Sussman, Joel L.
Submitted by:
the author.
(Entry 16). Submitted on May 4, 2008.
- Cross-indexing terms:
snapshots; jmol.
FirstGlance in Jmol offers one-click views of any molecule (PDB file) including secondary structure, ribbons, amino to carboxy (or 5' to 3') rainbow, Composition, Hydrophobic/Polar, Charge, Vines, and (under More Views..) Salt Bridges and Cation-Pi Orbital Interactions.
For details on these views, see the Snapshot Gallery.
The Contacts.. dialog enables close-up views of non-covalent interactions to any moiety (selected by clicking on it).
Portions of the molecule can be hidden (by clicking on them), and sequence positions or amino acids of interest can be located easily.
Instructions are provided for copying snapshots into Powerpoint, etc. FirstGlance in Jmol works in popular browsers in Windows, Safari on Mac OSX, and Firefox on linux.
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Author:
Martz, Eric
Submitted by:
the author.
(Entry 11). Submitted on Oct 21, 2006. Last revised on Oct 21, 2006.
- Cross-indexing terms:
rotatable, zoomable views; arbitrary views with complete control; Jmol.
Create rotatable, zoomable molecular views in Jmol without learning any programming or scripting languages. The molecular views are generated in Protein Explorer, where you have complete control including rendering, colors, orientation, and zoom level. Learning how to use Protein Explorer well will take a few hours. But then, saving a MolSlide takes just a few mouse clicks.
The MolSlide Manager (built into Protein Explorer) makes it easy to add text, including color keys, to rearrange your MolSlides, and to import and combine slides from different sets.
Using Protein Explorer (to create the views) requires a Windows computer with the MDL Chime plugin installed in the Firefox browser. However, Protein Explorer can save MolSlides in either MDL Chime, or Jmol. MolSlides that use Jmol can be viewed in Internet Explorer, Firefox, or Netscape on Windows, Safari on Mac OSX, and even Firefox on linux. You do NOT need Protein Explorer to view MolSlides, once created. See EXAMPLES OF MOLSLIDES.
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Authors:
Martz, Eric; Driscoll, Tim; Reichsman, Frieda.
Submitted by:
the author.
(Entry 8). Submitted on Oct 21, 2006. Last revised on Oct 21, 2006.
- Cross-indexing terms:
morphs; conformational change morphs; jmol; animations of conformational changes; molmovdb; motions, macromolecular; hingemaster; flexoracle; tlsmd; stonehinge; movies; conformation explorer; flexibility, molecular.
Submit two conformations (in PDB format) of the same molecule, and this server will produce an animated morph (interpolated movie) of the conformational change. Morphs can be viewed in Jmol or Chime (which enable the animation to be viewed from any perspective) or as true movies (such as multi-GIFs or MPEGs). There is a large database of previously-generated morphs in the Yale Database of Macromolecular Motions.
To see multi-GIF, MPEG and other movies, click the links to the old morph report.
Use the Hinge Prediction Server on the front page to predict the location of flexible points in single protein structures. This resource will run four hinge prediction algorithms on your structure: FlexOracle, StoneHinge, TLSMD, and NSHP, plus HingeMaster, which combines the four scores for superior results. You can view a graph of the results or get a publication-quality image of your structure colored by flexibility.
Coming soon: the Conformation Explorer, which will help predict ligand-induced motions based on a single submitted protein structure.
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Authors:
Gerstein, Mark; Flores, Samuel; Krebs, Werner; Echols, Nat.
Submitted by: Flores, Samuel.
(Entry 10). Submitted on Oct 21, 2006. Last revised on Oct 23, 2006.
- Cross-indexing terms:
membrane proteins, showing lipid bilayer position; Jmol.
This server shows the position of the lipid bilayer, and the orientations of transmembrane proteins, for any transmembrane PDB file. It generates a high-quality snapshot (such as the one at right), and you can also view the PDB file with pseudo-atoms added to represent the planes of the membrane surfaces, in Jmol, Chime, or Webmol.
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Authors:
Lomize, Andrei; Lomize, Mikhail; Pogozheva, Irina.
Submitted by: Martz, Eric.
(Entry 13). Submitted on Oct 21, 2006.
- Cross-indexing terms:
RasMol; multi-GIF generator; animations; rotating views; scriptable rotating views.
Generate a rotating molecular view (multi-GIF) using RasMol by filling in a simple form. You control the image size, speed of rotation, and axis of rotation, as well as the rendering and color scheme. Knowledge of RasMol script language is helpful for complete control, but is not required for basic images. An expert form allows different renderings in each frame.
Comment by Eric Martz (emartz@microbio.umass.edu) October 2006: This site is easy to use for beginners, yet offers power for those who know a little RasMol scripting language. Animations produced with PyMol using Polyview-3D (see below) have higher image quality.
Image at right by James Smith, from the PDB2MultiGIF gallery.
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Author:
Bohne, Andreas
Submitted by: Martz, Eric.
(Entry 9). Submitted on Oct 21, 2006. Last revised on Dec 13, 2006.
- Cross-indexing terms:
PyMol; RasMol; animations; multi-GIFs; publication quality.
Enter any PDB code (or upload a PDB file) and use a simple form to generate molecular views with PyMol (publication quality!) or RasMol. Proteins are shown as ribbons. Optionally, you can spacefill a designated chain, and/or label residues. You can also show only one chain, in which case (with PyMol) it is rendered as a surface. Several color schemes are available, and the background color is adjustable. You can set the pixel size of the animation; the static images are available as a high-resolution TIFF file. You set the smoothness and rate of rotation, and axis (or axes) of rotation in the animation. Sample results are shown so you can see what each option does, and there is extensive help.
Comment by Eric Martz (emartz at microbio.umass.edu) October 2006: Very easy for beginners to use. Highly recommended!
Limitations: None! The limitations mentioned here earlier have been removed (October, 2006). The author, Aleksey Porollo, is very responsive to feedback.
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Authors:
Meller, Jarek; Porollo, Aleksey; Adamczak, Rafal.
Submitted by: Martz, Eric.
(Entry 7). Submitted on Oct 21, 2006. Last revised on Oct 26, 2006.
- Cross-indexing terms:
movie making; animations; publication quality; docking animations; ligand binding animations.
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Protein Movie Generator (PMG) makes it easy to produce publication-quality still images of 3D protein structures, or a wide variety of movies and animations. You can easily make a ligand(s) fly in from the corner(s) and dock to a receptor. Or the protein can rotate or rock at a specified rate. Elaborate background images and shadow casting options are readily available. The results are gorgeous and are ready to drop into a Powerpoint presentation, or use in a journal publication.
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Authors:
Ludovic, Autin; Ludovic , Autin; Pierre, Tuffery.
Submitted by: Ludovic, Autin.
(Entry 15). Submitted on Nov 17, 2007. Last revised on Nov 20, 2007.
44 total subject cross-indexing terms.