[Chimera-users] ribbackbone

Edward J Brignole brignole at mit.edu
Tue Mar 29 09:54:22 PDT 2016

Dear Chimera developers and users,

I'm trying to make a figure that shows hbond contacts with a ligand but am having a problem displaying contacts while simultaneously displaying residues and ribbons. I know that ribbackbone will allow simultaneous display of ribbon and backbone, but the problem is that this attribute is set for the entire model, not per residue. To keep the display as uncomplicated as possible I want to just show side chains except when there's a backbone contact then I want to show backbone for that residue as well. The problem arises when contacting residues are adjacent, if ribbackbone is on, then the CA's are connected, but if I turn ribbackbone off then I lose the backbone atoms I'd like to show except an occasional floating carbonyl oxygen.

My workflow is basically:
sel #0:LIG
findhbond spec #0 sel cross intermodel F intraMol F intraRes F makePseudobonds T reveal T distSlop 0.7 angleSlop 40
ac cs
ribbackbone #0
transparency 75,r #0

I'm sure there's a way to accomplish this but I haven't been able to figure it out. I saw there has been some discussion previously on the chimera-users list about ribbackbone display but I didn't find any posts that would solve this particular problem. My apologies if this situation has already been discussed.

Thank you for your help,

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