I don't want to brag, but check out this beauty: http://iri-pc87.ulb.ac.be/sample/sample/test_jmol.html
;-) Joost >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 > > ----- ----- 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
