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.)