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Date: Mon, 14 Jul 2025 13:08:40 +0000 (UTC)

From: mariela Urrutia <urrugada@yahoo.com>

Subject: [chimerax-users] contacts

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Hello, Could you tell me please how to get the contacts of a residue in a list and in the molecule representation?Thanks you in advance.Mariela-------------- next part --------------

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Message: 2

Date: Mon, 14 Jul 2025 08:41:41 -0700

From: Elaine Meng <meng@cgl.ucsf.edu>

Subject: [chimerax-users] Re: contacts

To: mariela Urrutia <urrugada@yahoo.com>

Cc: "chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu>

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Hi Mariela,

That is a very broad question. There are several different ways and it depends exactly what you want.

However, one way is to make sure the atoms of the residue are displayed, then select the residue (Ctrl-click on one atom, keyboard up arrow to select whole residue so that it has a green outline), then use the Contacts tool, menu: Tools... Structure Analysis... Contacts.

See:

<https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html>

In the Contacts tool there are several options. You should use Limit by selection "with at least one end selected" so you will get only the contacts of that selected residue, and there also options to Write information to Log and/or File. If you also use the "Select atoms" option the contact atoms will become selected and you can do other things with them (label, color, etc.) using the Actions menu. See help link above for details. Here is more about selection and actions

<https://rbvi.ucsf.edu/chimerax/docs/user/selection.html>

<https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions>