[Chimera-users] [Chimera] Different bond width in the same model

Konstantin Richter konstantin.richter at bbz.uni-leipzig.de
Fri Oct 29 01:58:38 PDT 2021

Dear Elaine,
thank you for your help! The setattr command works perfectly.

best wishes
Konstantin Richter

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

> On Oct 28, 2021, at 4:56 AM, Konstantin Richter  
> <konstantin.richter at bbz.uni-leipzig.de> wrote:
>> Dear Elaine,
>> I am currently trying to create molecular figures with the old  
>> Chimera (not ChimeraX). I would like to represent different bonds  
>> in the same model in different bond widths: in my case, a disulfide  
>> bond should be represented thicker than the bonds of a nearby ligand.
>> I already learned that the bond width is the product of the stick  
>> scale (which is a model attribute) multiplied by the bond radius  
>> (which is an atom attribute, if I got it right):  
>> https://www.cgl.ucsf.edu/pipermail/chimera-users/2013-November/009289.html
>> So changing the bond radius for only the ligand atoms but not the  
>> disulfide atoms would do the job for me, right? Unfortunately I  
>> have no idea how to change the bond radius in the command line. Is  
>> there any command for that?
>> Thanks in advance for your help!
>> best wishes
>> Konstantin Richter
> Dear Konstantin,
> You can change the bond radius in the Selection Inspector (e.g.  
> select the part you want to change, then click the green magnifying  
> glass in the lower right).  In the Selection Inspector, inspect:  
> Bond, and then change the bond radius value for the current  
> selection.  If you hold the mouse over the "radius" part of that  
> dialog, a popup balloon says that the name of this bond attribute  
> (for using in commands) is "radius"
> If you prefer to use commands only, the command to set attribute  
> values is "setattr," e.g.
> setattr b radius 0.4
>  .... to change all bonds
> setattr b radius 0.1 sel
> ... to change bonds in the current selection (and you can use any  
> other atomspec, not just "sel", e.g. model numbers, residue names or  
> numbers, etc.)
> The general explanation of this and how to change it is
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#representations>
> Selection Inspector
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html#bondprop">
> setattr command
> <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

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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