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

Konstantin Richter konstantin.richter at bbz.uni-leipzig.de
Thu Feb 18 09:13:08 PST 2021

Hi Elaine,
that solved my problem! Many thanks for the quick response and best wishes.


Zitat von Elaine Meng <meng at cgl.ucsf.edu>:

> 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
> See:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
> I hope this helps,
> Elaine
> -----
> 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

P. Konstantin Richter - M.Sc. Biochemistry
Department of Structure Analysis of Biopolymers - Institute of  
Bioanalytical Chemistry
Center for Biotechnology and Biomedicine (BBZ) - Leipzig University
Deutscher Platz 5
D-04103 Leipzig

Tel.: +49 341 9731316

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