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

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

The default values of the "findclash" command are the recommended values for clashes (not contacts): <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> "For detecting clashes, a cutoff of 0.4-1.0 Å and a hydrogen bond allowance of 0.2-0.6 Å are recommended. The findclash command defaults are the same as the default clash criteria in the Find Clashes/Contacts graphical interface: 0.6 and 0.4 Å, respectively."

On Jul 1, 2024, at 9:04 AM, edith.gincel--- via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Thank you elaine

I saw

For detecting contacts, negative cutoff values of 0.0-(–1.0) Å with an allowance of 0.0 Å are generally reasonable (default contact criteria –0.4 and 0.0 Å, respectively).

So I thought that 0.0 was the default value and I didn't change it. Edith

I found the answer : IgnoreHiddenModels true Thank you anyway Edith