Hi Fernando, As you said, the ChimeraX "measure buriedArea" command options only allow listing and selecting the whole residues, not per-atom. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> However, I get a different result for the ligand-protein buried area than you do, so I may not be understanding your process. Here's what I get from open 4rsc delete /B measure buriedarea :a3v with protein Log says: Buried area between :a3v and protein = 376.72 area :a3v = 498.34, area protein = 19956, area both = 19700 If "measure buriedarea" assigned a per-atom buried area attribute you could then use a separate "select" command to select atoms by attribute value, but as far as I know it does not do that. Instead, you could simply use the "contacts" command to select atoms in the protein contacting the ligand based on interatomic distances and VDW radii, e.g. open 4rsc delete /B contacts :a3v restrict protein select true reveal true log true See <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> for options including saveFile. ... that also selects the ligand atoms that are contacting the protein atoms, but you can then deselect them, e.g. ~sel :a3v view sel ~ribbon label sel Note that this can also be done with the ChimeraX graphical interface, namely menu: Select... Contacts... (Atomic) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 7, 2024, at 10:33 AM, Fernando Villa via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera users I have been trying to select the atoms involved in the interface of a receptor/ligand complex in ChimeraX without success. In UCSF Chimera e.g. open 4RSC del solvent sel #0:.b del sel select ligand zr>10 del sel focus measure buriedArea protein ligand sel @/buriedSASArea “Only atoms at the interface are selected” = OK
**The interface buried area calculation was performed and the atoms involved in the buried area were selected.
However, I wish to do the same in ChimeraX, for surface area calculations: e.g. open 4RSC del solvent del /B select ::name="A3V" view sel measure buriedarea protein withAtoms2 ligand sel t list t cutoff 0 “All atoms in the interface are selected per residue” = KO
The results of the calculations are the following: UCSF Chimera = 719.643 ChimeraX = 719.65 = OK I have difficulties to select only the atoms in the interface, not all atoms of the residues, I have tried several ways to do this but it has been complicated, I even tried to insert the command “sel @/buriedSASArea” of UCSF Chimera in ChimeraX without success.
Sincerely.
Fer
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