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<div class="elementToProof"><span style="font-family: Verdana, Geneva, sans-serif; font-size: 14pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">Dear Elaine,</span></div>
<div class="elementToProof"><span style="font-family: Verdana, Geneva, sans-serif; font-size: 14pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">thank you. It worked.</span></div>
<div class="elementToProof"><span style="font-family: Verdana, Geneva, sans-serif; font-size: 14pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">Best regards and merry Christmas,</span></div>
<div class="elementToProof"><span style="font-family: Verdana, Geneva, sans-serif; font-size: 14pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">Luigi<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Tuesday, December 13, 2022 00:31<br>
<b>To:</b> Luigi Marongiu <luigi.marongiu@outlook.com><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Primer in chimeraX</font>
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<div class="PlainText">Hi Luigi,<br>
(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.
<br>
<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html">https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html</a>><br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume">https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume</a>><br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/measurevolume.html">https://rbvi.ucsf.edu/chimerax/docs/user/tools/measurevolume.html</a>><br>
<br>
The Volume Viewer is something different, that is a tool for viewing "volume data" like density maps.<br>
<br>
(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.<br>
<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html">https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html</a>><br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/hbonds.html">https://rbvi.ucsf.edu/chimerax/docs/user/tools/hbonds.html</a>><br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html">https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html</a>><br>
<br>
See also tutorial: Protein-Ligand Binding Sites<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html">https://rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Dec 12, 2022, at 4:10 AM, Luigi Marongiu via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> <br>
> Dear sir/madam,<br>
> I am new in the use of ChimeraX (for Linux).<br>
> I would like to use ChimeraX for two jobs:<br>
> • 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?<br>
> • 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?<br>
> Thank you.<br>
> <br>
> Best regards,<br>
> <br>
> Luigi Marongiu<br>
> Ph.D., B.Sc. (Hons.)<br>
<br>
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