Hello Eliane, first of all thank you alot for your help... i am grateful. i will check now and try the instructions that you shared and i will get back to you if my problems persists. Regards, Christian ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, February 20, 2025 7:28 PM To: FRANGIE Christian <christian.frangie@ulb.be> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: listing contact residues in ChimeraX Hi Christian, (I added a descriptive Subject line... this is useful for our archive) There are several different ways you could do this, with various GUIs or commands. It depends how you want to define contacts. If by atom-atom distances and atomic VDW radii, you could use the "contacts" command or Contacts tool. If by whole residues and buried surface area, you could use "interfaces" command. <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fclashes.html&data=05%7C02%7Cchristian.frangie%40ulb.be%7C74aba6105b874e51671108dd51dc76ea%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638756729517036591%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=dgLThlXyfBvDfNpwiNiIYY03nTsAvvpJKO0%2Fs9Fj5MM%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fclashes.html&data=05%7C02%7Cchristian.frangie%40ulb.be%7C74aba6105b874e51671108dd51dc76ea%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638756729517057997%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=8PwaDTPg%2FyU%2BRbsE6A%2FkfcP926j4lVEDLG%2BLptaMEs0%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Finterfaces.html&data=05%7C02%7Cchristian.frangie%40ulb.be%7C74aba6105b874e51671108dd51dc76ea%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638756729517070680%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=DxVaavJH7WubAF%2BqftGnieVXHUBwC1vmpiHH4ctyGoo%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html>> Both of the above provide ways of selecting the contact atoms or residues, and "contacts" also has options to write info to file and the Log. There is also menu: Select.... Contacts... which gives an interface to both ways. If you choose "Chains" in the dialog you can use the buried surface-area method or distance. If you choose "Atomic" it will use a subset of the options in the Contacts tool. Details: <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fselectcontacts.html&data=05%7C02%7Cchristian.frangie%40ulb.be%7C74aba6105b874e51671108dd51dc76ea%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638756729517082679%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=7xXp7lY%2BNRVBsiHGnC%2BVMb2VPXsw7838vqMmRZiEw%2FE%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html>> The GUIs may be friendlier for you to use at first, but they will also show the corresponding command in the Log so that you can learn the commands if you want. The commands are much shorter to describe in email, however. Here is an example of the contacts command, to list pairwise atomic contacts between protein parts of C vs. (A+B) contacts /C & protein restrict ( /A,B & protein ) reveal true log true saveFile ~/Desktop/c-ab-atompairs.txt There are adjustable parameters and other options to all of these approaches, and you would change the file location and name as appropriate for your system. See help links above for details. If you don't care about the pairwise interaction information and you only want lists of residues, there is one way to do it with the "contacts" command: contacts /C & protein restrict ( /A,B & protein ) reveal true select true select up info residues sel saveFile ~/Desktop/c-ab-residues.txt ... or you can omit the saveFile stuff to just show the list in the Log instead of writing it to ~/Desktop/c-ab-residues.txt -- see "info" help <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Finfo.html&data=05%7C02%7Cchristian.frangie%40ulb.be%7C74aba6105b874e51671108dd51dc76ea%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638756729517094471%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=THOG8EUtR0qJNwT%2FrtP1H3%2BARjNdCKrTTxWj9No474Q%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html>> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 20, 2025, at 5:34 AM, FRANGIE Christian via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear UCSF ChimeraX Support Team,
My name is christian frangieh, I am currently using chimera x and i want to check the interacting residues that form the interface between 1 chain with 2 other different chains. for example my model has 3 chains (chain A,B,C) i want to have a list of the resideus of chain A and B that are interacting with chain C Can you please help me with this?
Thank You