[Chimera-users] Selecting bonds/pseudobonds with a cutt-off distance

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 23 07:46:30 PDT 2019

Hi Yasser,
Sorry, Chimera does not include a command or tool to select bonds or pseudobonds by length.  There might be something similar in the Chimera plugins on the web (developed by others), say Xlink Analyzer, but I don’t know for certain:

If you use ChimeraX instead, it can be done for pseudobonds (but not bonds) with the “select” command and the “minimumLength” and/or “maximumLength” option, see:

In ChimeraX you can also display an interactive histogram of pseudobond lengths with the “crosslinks histogram” command, as shown here for H-bonds:

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

> On Aug 23, 2019, at 4:31 AM, Yasser Almeida Hernández <yasser.almeida at gmail.com> wrote:
> Hi all,
> how can I select bonds/pseudobonds with a cutt-off distance, say bonds/pseudobonds with more than/less than X?
> Thanks in advance,
> Yasser

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