Okay, I think this is the way to go. I tried it on the file with 7 rotamers and it works fine. I have a program that generates the PDB file and I can add anything to the file output I want, so if I tell it to write MODEL1 ... ENDMDL for each model, it should work.
Thanks for all the help! Saved again. ;-) cheers, Joost >As Miguel suggests and my demo shows, the thing you need to do is to separate >the different models using > >MODEL >ENDMDL > >as shown, for example, at > >http://rcsb-deposit.rutgers.edu/adit/docs/pdb_atom_format.html > > 1 2 3 4 5 6 7 > 8 >12345678901234567890123456789012345678901234567890123456789012345678901234567890 >MODEL 1 >ATOM 1 N ALA 1 11.104 6.134 -6.504 1.00 0.00 N >ATOM 2 CA ALA 1 11.639 6.071 -5.147 1.00 0.00 C >... >... >ATOM 293 1HG GLU 18 -14.861 -4.847 0.361 1.00 0.00 H >ATOM 294 2HG GLU 18 -13.518 -3.769 0.084 1.00 0.00 H >TER 295 GLU 18 >ENDMDL > >Of course the catch is that with this you need to duplicate ALL the entries. >A nice benefit of this is that then you can run the animations and watch your >rotomers interconvert. > >With 80+ rotomers that's a BIG file. You might consider doing this in a way >I've >done, where the single file is read in, then parsed, then reloaded as a set of >models. The JavaScript sequence for this is really not that bad: > >strModel="" >Model=new Array() > >function mycallback(app,msg){ > var strMsg=msg+"" > if(strMsg.length<1000)return > strModel=strMsg > Model=strModel.split("TER") > strModel="" > for(var i=1;i<=Model.length;i++){ > strModel+="MODEL "+i+"\n"+Model[0]+Model[i]+"ENDMDL\n" > } > setTimeout("document.jmol.loadInline(strModel)",100) >} > > >This is a bit crude, but I think it does the job. (It doesn't rip out the >Tyr A 155, though. If that's really what you need, that's a bit of a problem, >I >think. > >One PARTIAL solution, actually a pretty nice one would be an option in Jmol >such > as > >set interchainbonding ON/OFF > >This would, I guess, have to be executed BEFORE a "load" command and would >direct the bond-generator to NOT connect atoms that are in separate TER sets. >What this would allow is for you to load your model with all those sets just >the >way you have them and then restrict them to separate rotomers by defining >groups >of atoms as, for example: > >define mainchain 1-210 and not 155 >define rotomer1 (mainchain or 1210) >define rotomer2 (mainchain or 1211) >define rotomer1 (mainchain or 1212) >... >restrict rotomer1 > >except... How do you "unrestrict"? So that then later you can do: > >restrict rotomer2 > >etc. > >This will ONLY work if Miguel can allow for ignoring interchain bonding. > >Bob > > > > > > > >Joost Van Durme wrote: > >> Hello! >> >> I'm investigating rotamer distributions of residues and I write a new PDB >> file including the found rotamers for one position. These are written at the >> end of the PDB file. The result is that multiple rotamers of one residue are >> displayed in the molecule. Unfortunately, Jmol starts to make bonds between >> those rotamer atoms, and that's not really what I want. It gets pretty messy >> that way. >> >> Is there a way to get this fixed? Or a workaround somewhere? >> >> you can view the model here: >> http://iri-pc87.ulb.ac.be/sample/sample/test_jmol.html >> >> and download the PDB file here: >> http://iri-pc87.ulb.ac.be/sample/sample/JOOST.PDB >> >> For info, you see the rotamers of a Tyrosine. ;-) >> >> Joost >> >> >> >> ------------------------------------------------------- This SF.Net email is >> sponsored by Oracle Space Sweepstakes Want to be the first software developer >> in space? Enter now for the Oracle Space Sweepstakes! >> http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click >> _______________________________________________ Jmol-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users > >-- > >Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 >Professor of Chemistry, St. Olaf College >1520 St. Olaf Ave., Northfield, MN 55057 >mailto:[EMAIL PROTECTED] >http://www.stolaf.edu/people/hansonr > >"Imagination is more important than knowledge." - Albert Einstein > > >------------------------------------------------------- >This SF.Net email is sponsored by Oracle Space Sweepstakes >Want to be the first software developer in space? >Enter now for the Oracle Space Sweepstakes! >http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ----- ----- Interdisciplinary Research Institute for Human and Molecular Biology (IRIBHM) Faculty of Medicine Free University of Brussels Belgium ----- d(^_^)b ------------------------------------------------------- This SF.Net email is sponsored by Oracle Space Sweepstakes Want to be the first software developer in space? Enter now for the Oracle Space Sweepstakes! http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
