Hi Bob, mmm, this is not good. I guess that if Jmol always connects close atoms (no matter what the occupancy is), there is no way to read in such a PDB file with several rotamers that are duplicates of one position.
It also doesn't matter whether TER between the rotamers is there or not, so it seems. I believe that the only solution would be to tell Jmol not to connect a Tyr ring to another Tyr ring or simply, not to make weird bonds between amino acids. But then again, I'm the one doing something weird to the PDB file. Mmm, pitty ... I'm gonna be stuck on this one for a while ... Thanks for the help already, Bob. And by the way, I reduced the number of rotamers in the PDB link below, just to clear up some things. http://iri-pc87.ulb.ac.be/sample/sample/test_jmol.html http://iri-pc87.ulb.ac.be/sample/sample/JOOST1.PDB Joost >Joost, I was playing with your file. Check out: > >http://www.stolaf.edu/people/hansonr/jmol/test/test_jmol.html > >Here's the deal: > >You are using TER to set off those rotomers. This won't work for two reasons. > >First, Jmol is connecting all close atoms, so you are seeing lots of connected >atoms. Not only that, though, there's a limit on number of bonds, and since you >are exceeding that in the basic model, you won't ever be able to see the bonds >the way you expect. > >Second, Jmol can't read "TER" anything more than "termination" > >My fiddling suggests that you need to reconsider how you create this file. >One problem is that the different "TER" block tyrosine residues are duplicates >of Tyr A 155. So it's not clear how you would remove that group and show the >others. (In the animation above, I removed it manually.) > >So I think it's up to you to create a model file with more standard format. > >Bob Hanson > > > >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 > > ------------------------------------------------------- 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
