Hello Edith, I meant that you have to go through all of the command options yourself and see that they are same as the settings in the GUI (tool), not that we would figure it out for you. I can't tell whether you really chose the exact same atoms #0 to test atomic contacts against #1 in the tool. However, even from the few things that you did mention, if you have "subtract 0.0 ..." in the tool then you would need to use the command option "hb 0.0" to do the same thing because the default is 0.4. See the manual pages for the tool and command for explanations of all of the options in each, and what the default values are: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> The tool and command will give you exactly the same answer as each other if you use exactly the same atoms, same options, and same parameter values. In ChimeraX it would be much, much easier to make sure they are the same because when you use the tool, the command from runing the tool is automatically shown in the Log. You may want to switch to ChimeraX in the future. 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, 2024, at 5:52 AM, edith.gincel--- via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Thank you for your answer (sorry for the delay, I was not working for 3 days)
I am using chimera (not chimeraX), but I could change if needed
The command I use is this one : open 1 fic.mol2 ; findhbond intramodel false saveFile LHfic ; findclash #0 test #1 overlapCutoff 0.0 saveFile contact_fic; close 1
when I use the menu: - Find clashes/contact Atoms to check : second set of designed atoms Clash/contact parameters : Find atoms with vDw overlap 0.0 angsrom substract 0.0 from overlap ....
I supposed it should do the same, but maybe not....
Edith