I just noticed this thread. Since I've done dozens of interpolated animations in Chime, I'll add my 2 cents.
1. I would be pleased to see a simple linear interpolation option built into Jmol. The need for such "morph" animations is becoming more common as more structures are solved in different conformations. Having it built into Jmol would save a lot of time and make this kind of visualization more accessible to a much wider authorship. 2. I'm not convinced that spline smoothing or other more complicated options are worthwhile. When something more than a simple linear interpolation is needed, what is needed is usually much more complicated than smoothing. In my mind, there are three categories of conformational changes from the perspective of visualization: A. Small movements of a few residues that can be satisfactorily visualized by simply toggling back and forth between two models (empirically known, or theoretical). An example is the changes in antibody sidechain positions when antigen binds. B. Larger movements that require interpolation (morphing) in order to understand the changes in conformation. The first morph I did (recoverin +/- calcium) illustrates such a case (URL below). C. Huge movements that require that intermediate key frames be manually modeled in order to produce a useful morph. Simple linear interpolations may move domain in implausible directions, or move domains through one another. Positioning the domains in reasonable intermediate key frames, then interpolating between these key frames, gives a more useful result. An example is RNA polymerase (look for the "movie" and "animation" links at http://www.chem.umass.edu/~cmartin/ -- this is not in Chime or Jmol -- evidently they didn't publish that form?) Another dramatic example that I have long wanted to see done well is the inactivation of trypsin by a serpin. As far as I recall, it hasn't been done. For categories B and C, a linear interpolation usually has clearly bogus intermediates, such as the collapse and reexpansion of domains, the formation of "cobweb clumps" of bogus covalent bonds when atoms move too close to each other, or the passing of one chain through another. The latter occurs in my recoverin morph. These "chemically impossible" intermediates are still often compatible with a large advantage for effective comprehension of the conformational changes. Further, they serve to remind the viewer that the intermediates are not attempts to predict the true trajectory of change, but simply visual aids. When one wished to go beyond linear interpolation, the next step is to do molecular mechanics/dynamics on the interpolated intermediates to make each step "chemically possible". Luckily, years of work on such routines have been provided as a free server by Werner Krebs, Mark Gerstein, and Nat Echols, the Yale Morph Server (http://www.molmovdb.org/morph/). At their Database of Macromolecular Movements (molmovdb.org) you can also find hundreds of morphs done by visitors to the site, shown in Jmol or Chime or Protein Explorer. Doing a morph with this server takes a bit of time, so I always try linear interpolation first. 3. MORPH RESOURCES (not linked above): My original Protein Morpher. This has linear and minimized interpolations of recoverin, integrin CD11b MIDAS domain, influenze hemagglutinin, calmodulin, cAMP kinase. It is available through MolviZ.Org, or go directly to http://www.umass.edu/microbio/chime/morpher/index.htm Unfortunately, it ONLY WORKS IN NETSCAPE 4.8 with CHIME. However, if you don't want to install Netscape 4.8 (instructions: http://www.umass.edu/microbio/chime/neccsoft.htm#browsers ) and Chime, you can still read: Morph Rationale and History (First? Morph): http://www.umass.edu/microbio/chime/morpher/fs_mtop.htm and Morphing Methods: http://www.umass.edu/microbio/chime/morpher/morphmtd.htm ------------------ Protein Explorer has a control panel named "NMR Models/Animation". If a morph is provided as an NMR-style multiple model PDB-format file, Protein Explorer can animate it. As you likely appreciate, displaying an animation in Chime or Jmol means you can rotate it to view the animation from different perspectives, and change the color scheme or rendering. These are in contrast to an animated GIF (true movie) which has only a single color scheme, rendering, and perspective. Protein Explorer has convenience buttons to use common color schemes and renderings for the animations. There is a script box in which you can customize the animations. Protein Explorer displays the animation in a separate browser window, which can be saved to disk. This enables the animation to be played separately, without Protein Explorer. To see many examples (as animated GIFs, and as interactive PDB file morphs), go to ProteinExplorer.Org and at the FrontDoor, click on Morphs. Or go directly to http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/morfdoc.htm Since Protein Explorer works in Windows Firefox, Internet Explorer, or Netscape 7.2, so do these examples (also Mac Classic with Netscape 4.8). ------------------ It has been on my To Do list for some time to enable Protein Explorer to export its animations in Jmol as well as Chime. If anyone cares to help by taking a Chime animation and converting the script for Jmol, I'll apprecate the help. Protein Explorer can already export most molecular views into MolSlides in Jmol (as well as Chime). The views in sets of MolSlides can be rotated and zoomed. Examples in both Jmol and Chime are at http://molslides.proteinexplorer.org ------------------ I wrote a small program in C, and compiled it for MS-DOS, that does linear interpolations. Input is two PDB file models (the end states of the morph) and you specify the number of frames in between that you want (generally with more than 15, Chime performs the animation too slowly). Output is in NMR (MODEL/ENDMDL) format PDB files, ready for Protein Explorer. This and other PDB file manipulation tools are downloadable here: http://www.umass.edu/microbio/rasmol/pdbtools.htm ====================== Incidentally, I am thrilled to see the Jmol project moving forward with such vitality, and with contributions from such a large and diverse volunteer group. Unfortunately, I can't keep up with jmol-users. When I know a lot about the topic, it takes me an hour to add my 2 cents. When I don't, it takes me many hours of research to contribute. So although I am intensely interested, I am happy that I am dispensible, and I look forward to using enhanced versions of Jmol resulting from the jmol-user discussions as they become available. And to help from jmol-users!! I do expect that most of my future work will be Jmol-based. I am also pleased to say that several other journals are in stages of adopting FirstGlance in Jmol for their on-line readers. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://workshops.proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.proteinexplorer.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ------------------------------------------------------------------------- Take Surveys. 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