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
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://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> <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://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://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
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
Hello again Eliane. Sorry for bombarding you with the emails. Can you please elaborate more on this idea "If by whole residues and buried surface area, you could use "interfaces" command", can you give me an example of commands just like you did with the contacts. In addition if i have an amino acid (residue) and i want to check whether a mutation and a change in the residue causes the residue to change its exposure to the surface (for example the wild type a.a was buried the mutant a,a became surface exposed) what are the commands that i should use. Thank you again for your patience and understanding and collaboration. 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
I meant you will not get information on the specific pairwise atom-atom interactions. Instead you will get just the whole residues with buried surface area. You should just try the menu approach I already told you and it will show you the commands in the Log. Example: open 2hhb Menu: Select... Contacts... ... in the dialog use the "Chains" section and on the left choose chain /C and on the right choose chains /A and /B. Use default options under there (select contacts in both, buried solvent-accessible surface area blah blah), click OK. The "interfaces" command it uses will be shown in the Log. These are all explained in the help links I sent earlier. Then you have a set of selected residues and you can use "info residues sel" just like in the previous example. Elaine
On Feb 21, 2025, at 7:11 AM, FRANGIE Christian via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello again Eliane.
Sorry for bombarding you with the emails. Can you please elaborate more on this idea "If by whole residues and buried surface area, you could use "interfaces" command", can you give me an example of commands just like you did with the contacts. In addition if i have an amino acid (residue) and i want to check whether a mutation and a change in the residue causes the residue to change its exposure to the surface (for example the wild type a.a was buried the mutant a,a became surface exposed) what are the commands that i should use.
Thank you again for your patience and understanding and collaboration.
Regards, ChristianFrom: 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....> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....>
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....>
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....>
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
-
Elaine Meng -
FRANGIE Christian