Hi Jerod, In general you would select the residues and then write a list of what was selected. There are several different routes to basically the same thing. All of them are described in the User Guide. I'll just mention a couple here: (A) You could simply use a zone selection in the command line. I can't give you the exact command since I don't know what specifies the ligand in your case, but if receptor were #1 and docked ligand of interest #2.16 then it could be something like the following to select all receptor residues within 5 Ang of the ligand: select #1 & #2.16 :<5 Then write the selection, e.g. to Log: info residues sel ... or to a text file info residues sel ~/Desktop/junk.txt See command-line zone spec <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones> See info command help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html> (B) You could first select the ligand somehow, <https://rbvi.ucsf.edu/chimerax/docs/user/selection.html> ...many ways described in link above, such as by Ctrl-click and up-arrow, or using the Select menu, or the "select" command, e.g. select #2.16 ... then use menu: Select... Zone, choose option to select "residues" ... this will select nearby residues in ALL models, however, so if you have other docked ligands all in the same place it would select those too and you might want to use method (A) instead. <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#select> Then when you have the residues of interest selected, use "info" as in method (A) to write the list. Yet other ways could be to use menu Select... Contacts, etc. <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> See also the "protein-ligand binding sites" tutorial <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> 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 Jul 1, 2025, at 10:46 AM, Denton, Jerod S via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, We are trying to see/export a list of amino acids that are within 5 angstroms of a docked ligand. Can you please tell me how to do this if possible? Thanks, Jerod Denton Vanderbilt