[chimerax-users] Primer in chimeraX

[Luigi Marongiu]

Dear Elaine,
thank you. It worked.
Best regards and merry Christmas,
Luigi
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Tuesday, December 13, 2022 00:31
To: Luigi Marongiu <luigi.marongiu at outlook.com>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Primer in chimeraX

Hi Luigi,
(1) calculate volume of molecule.  You would need to first show the molecular surface (menu: Actions... Surface... Show, or command "surface" or click the icon that shows surface), and then measure the volume inside the surface (menu: Tools... Volume Data... Measure Volume and Area, or command "measure volume #1" assuming the model is #1).  The value is reported in the Log and units of volume are cubic angstroms.

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/measurevolume.html>

The Volume Viewer is something different, that is a tool for viewing "volume data" like density maps.

(2) If you mean H-bonds, see "hbonds" command or H-Bonds tool (menu: Tools... Structure Analysis... H-Bonds).  To look for contacts there is also a Contacts tool in the same part of the  menu.

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

See also tutorial: Protein-Ligand Binding Sites
<https://rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html>

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

> On Dec 12, 2022, at 4:10 AM, Luigi Marongiu via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> Dear sir/madam,
> I am new in the use of ChimeraX (for Linux).
> I would like to use ChimeraX for two jobs:
>        • calculate the volume of a molecule (namley: maltose). I have uploaded the pdb of the molecule, selected the tools>volume>volume viewer, but I don't see any actual output. How can I get the value for the volume of this molecule?
>        • show the docking of a ligand. I have obtained a docking model with swissdock, which I have loaded; how can I show the bonds between target and ligand?
> Thank you.
>
> Best regards,
>
> Luigi Marongiu
> Ph.D., B.Sc. (Hons.)

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