[Chimera-users] ribbackbone

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 29 14:02:15 PDT 2016


Hi Ed,
No need to apologize!  I’ve often struggled with similar issues, and depending on the situation have resorted to combinations of ribbackbone, displaying only specific atoms, and in the worst cases, having two copies open of the same structure, one with ribbackbone and one without.  We’ve definitely put thought into doing some things differently in our next-generation program under development, e.g. allowing per-residue controls for making it look good where atomic detail is combined with ribbons.

I can at least solve the auto-chaining problem where adjacent CAs become connected.  You can turn off auto-chaining in the model attributes, or by selection/inspection of the molecule model, or with a command such as:

setattr m autochain 0

I don’t know if that fixes everything you'd hoped to fix.  

When ribbackbone is on, for residues where I need just the sidechain, I use “ball” style for CA atoms to obscure any offset from the ribbon, and undisplay N,C,O.  Unfortunately that doesn’t help the places where you need to show N,C,O because of H-bonds to the ligand.  If there are sidechains that look much, much better attached to the ribbon without ribbackbone (with backbone atoms hidden), you could try opening two copies and showing only the atoms/bonds of residues for which you need to show backbone from one copy, plus ribbons and the residues for which you need only sidechains from the other copy.   Sorry this solution is so kludgy.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Mar 29, 2016, at 9:54 AM, Edward J Brignole <brignole at mit.edu> wrote:
> 
> 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,
> 
> Ed



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