Selecting bonds/pseudobonds with a cutt-off distance
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
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: <http://www.rbvi.ucsf.edu/chimera/plugins/plugins.html> 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: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html#new> In ChimeraX you can also display an interactive histogram of pseudobond lengths with the “crosslinks histogram” command, as shown here for H-bonds: <http://www.rbvi.ucsf.edu/chimerax/features.html#hbond-histogram> I hope this helps, Elaine ----- 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@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
Thanks a lot! On 23.08.2019 16:46, Elaine Meng wrote:
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: <http://www.rbvi.ucsf.edu/chimera/plugins/plugins.html>
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: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html#new>
In ChimeraX you can also display an interactive histogram of pseudobond lengths with the “crosslinks histogram” command, as shown here for H-bonds: <http://www.rbvi.ucsf.edu/chimerax/features.html#hbond-histogram>
I hope this helps, Elaine ----- 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@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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Elaine Meng -
Yasser Almeida Hernández