[Chimera-users] Hide (pseudo-)bond between neighboring residues

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 18 08:58:42 PST 2021

Hi Konstantin,
There is "autochaining" between adjacent alpha-carbons, which produces these pseudobonds.  You can either turn off autochaining entirely, or you can turn off the display of any specific one.  Just select the pseudobond (Ctrl-click) and then use the green magnifying glass icon on the lower right corner of the Chimera window to bring up the Selection Inspector.

In the Selection Inspector,  if you change to "Inspect:  Pseudobond" then you can change "displayed" to "false" instead of "if atoms shown."  That is how to hide the specific selected pseudobond.  Or, you can change to "Inspect: Molecule model" and then change "auto-chaining" from "on" to "off" to get rid of all autochain pseudobonds for the whole model.  You can also do these things with the "setattr" command, e.g.: 
setattr m autochain false


I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 18, 2021, at 3:22 AM, Konstantin Richter <konstantin.richter at bbz.uni-leipzig.de> wrote:
> Dear Chimera Community,
> I currently experience some trouble hiding certain bonds that Chimera automatically displays. But first things first:
> I want to design a figure of the active site of two very similar protein structures (models #0 and #1; let's assume they are mutants of the same molecule differing in only a few amino acid residues). I therefore display the ribbon as well as certain residues of model #0. Additionally, I align #1 on #0 and display the same residues in #1, but without the ribbon. So, the side chains of #1 should end in the ribbon of #0 (which is basically identical to ribbon #1). Since Chimera automatically displays all atoms of the residues when the respective ribbon is hidden, I also hide C,O,N of #1 residues. Now this looks fine expect for one thing. Chimera creates long (pseudo?)bonds between the CA atoms of residues that follow one another in sequence, e.g. res 64 and 65. This very long 'bond' messes up my figure, and I haven't yet figured out how to delete or hide it.
> I already tried the ~bond #1:64-65 at CA command, but this one hides ALL bonds in residue 64 (but not the one between 64-Ca and 65-Ca) and other variations of the atom specifier. Is something wrong with my atom specification, or is this command not suitable for what I want to do? I also tried the bonddisplay command without succes, since it deletes all bonds in one residue.
> In the end, I want the residues of #1 to contain all atoms except for C,N,O including bonds between all atoms, but not the elongated connection between Ca atoms.
> best regards
> Konstantin Richter

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