Hi Edith, First be sure of whether you are using Chimera or ChimeraX. I will answer for Chimera because you sent this question to the chimera-users address. You can use either the tool in the menu (Tools... Structure Analysis... Find Clashes/Contacts) or the command "findclash" ... see the help pages for how to use them: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> Although they would get the same result if you used exactly the same options, parameter values, and atoms to check, you would get a different answer if any of those are different between the tool and command. So you need to figure out what was different. Maybe you turned on some option in the tool, for example, but did not use the command option that means the same thing. In ChimeraX it would be easier to figure this out, because when you use the ChimeraX tool it shows the command for that exact calculation in the Log. 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 Jun 26, 2024, at 9:25 AM, edith.gincel--- via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear all I am trying to check contacts between ligands and protein. I tried to use the command line, to be able to do it semi-automatically, but I don't find any contact. When I use the command line, I find contacts. Has someone experienced such problems? Thank you for your help