Miguel, Thanks for your quick response. I'll try to answer some questions:
> I haven't heard from you for a while. Well, as a non-biochemist and -crystallographer I followed the discussion from a distance for a while, hoping it would return to the xyz-animation one day...... And it did. > Please confirm that the m-xyz is the *only* type of animation file that > Chime supports. Well, I thought so, however: > However, Jan Reichert pointed out a web site which does have some .pdb > files which have individual frames stored as MODELs: > http://molmovdb.mbb.yale.edu/molmovdb/ > > They are somewhat hard to find, but they call them 'interpolation as NMR > format PDB file'. > I think Jan is the person to confirm or deny that PDB Models are used for animations. At his site there are morphed structures, and bundles in Protein Explorer, I couldn't locate a 'proper' pdb animation though. Great site by the way. > I do not understand what this Chime command is supposed to do. > Is it the case that when nmrpdb=false then only the first model is loaded? > I cannot imagine what auto/true are supposed to do. Quote from the manual: nmrpdb=true "sets the MIME type to the NMR-PDB mime type so that multiframe pdb-files can be loaded." This suggest that =false will result in loading the first structure only. See next answer. > Q: Is there some other way to identify a pdb MODEL, other than by model > number? > > Q: In Chime, can you only show one model, or can you show several ... as in: > model 2,3? This I have to try, never used it myself. > It looks simpler to me than a full-fledged animation because I do not have > to deal with multiple frames of atoms. I only have to deal with multiple > frames of display. Ah yes, I understand. I hadn't realized that you create the animation without the m-xyz file as an intermediate step, that there is a difference between "display frames" and "frames of atoms". So my suggestions as to what to do first do not apply. Let me just say that I'd like to see the animation control functions implemented. But I made that point already, I think..... And while we are at it, about the questions you asked Oliver: > Q: How do the scripting commands affect animations? > Q: When you apply commands like 'wireframe 0.1' does it affect all the > atoms in all frames? Yes. If you "select atomno=5; color atoms blue" atom 5 is coloured blue in all frames. > > Q: Is there a way to selectively address individual frames (or perhaps > better said, the atoms of individual frames) of an animation? No. You can display a frame ('anim frame 17' will display frame 17), but not selectively address 'atomno=5 in frame 17'. > Q: What do ping and pong do? Ping and pong are synonyms for palindrome, an animation mode that shuttles form 1 to end and back to one. Loop is the mode that runs repeatedly from one to end, one direction only. And while mentioning Oliver, with whom I share an interest: is implementing the MOPAC (and/or Gaussian) z-matrix format still on the to-do list? Hens ------------------------------------------------------- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps & Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
