[Chimera-users] [Chimera] Different bond width in the same model
konstantin.richter at bbz.uni-leipzig.de
Fri Oct 29 01:58:38 PDT 2021
thank you for your help! The setattr command works perfectly.
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):
>> 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
> Selection Inspector
> setattr command
> I hope this helps,
> 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
Center for Biotechnology and Biomedicine (BBZ) - Leipzig University
Deutscher Platz 5
Tel.: +49 341 9731316
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