[Chimera-users] how to load pseudobonds from command line?

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 12 10:03:23 PDT 2019

Hi Michał,
There are two general approaches, and only the second one is command-line:

(1) create a separate pseudobond file and then read it in with the Pseudobond Reader tool.

(2) use the “distance” command.  

You can hide the distance labels, change color, style (dashes/dots/solid lines) etc. with the “setattr” command, for example

setattr p color orange
setattr p label ‘'
(...that is supposed to be two single quotation marks with no space between, my Mail tool may make it fancy so it doesn’t work with cut-and-paste)
setattr g lineWidth 3

… and the setattr commands can have an atomspec at the end if you don’t want to change all pseudobonds, only the ones among the specified atoms.

If your script is python, it could do the reading of the pseudobond file using the Pseudobond Reader code, but somebody else would have to advise on the specifics.

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

> On Mar 12, 2019, at 6:07 AM, Michał Kadlof <m.kadlof at cent.uw.edu.pl> wrote:
> Hello,
> I'd like to display my psudobond in chimera script. How can I do it?
> --
> regards
> Michał Kadlof <m.kadlof at cent.uw.edu.pl>

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