Dear sir/madam, I am new in the use of ChimeraX (for Linux). I would like to use ChimeraX for two jobs: 1. 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? 2. 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.)
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@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.)
Dear Elaine, thank you. It worked. Best regards and merry Christmas, Luigi ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, December 13, 2022 00:31 To: Luigi Marongiu <luigi.marongiu@outlook.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@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@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.)
participants (2)
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Elaine Meng -
Luigi Marongiu