Hi How do I get a text file of contacts A-B (NOT A-A or B-B). I have tried Show atoms Select Contacts Chain A on left. Chain B on right Uncheck intermodel Check file. Please help. Thanks. Rosy
Hi Rosy, Sounds like you want inter-chain (A <-->B), not intra-chain. There are several possible ways. One way is just command contacts /A restrict /B saveFile browse ...where "browse" means to open file browser dialog to specify file name/location interactively. Or you can just give the file name and location directly, for example: contacts /A restrict /B saveFile ~/Desktop/ABcontacts.txt There are lots of other command options if you want to change any of the detection criteria and display parameters, use command "help contacts" or see the copy of the manual page at our website: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> You can do exactly the same thing with the Contacts tool, menu: Tools... Structure Analysis... Contacts, but you would need to first select one of the chains, e.g. A, and then choose the option in the Contacts tool: Limit by selection: between selection and atom spec... and enter "/B" in the box to the right of that, and check the "File" option like you said. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> You can also do it by first selecting chain A, then using menu: Select... Contacts, then choose Atomic tab and then use the same "Limit by selection" stuff as mentioned above. However, you would need to also click "Show Contacts tool" so that you could turn on the File option. <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> The intermodel thing doesn't matter if you only have one model (if you only opened one structure file). If you have more than one model you may need to specify which one, for example command: contacts #1/A restrict #1/B [... other options...] ...and "#1/B" as the atomspec to limit in the dialogs mentioned above. 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 Dec 5, 2024, at 5:01 AM, Rosaleen Calvert via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi How do I get a text file of contacts A-B (NOT A-A or B-B). I have tried Show atoms Select Contacts Chain A on left. Chain B on right Uncheck intermodel Check file. Please help. Thanks. Rosy
Hi Elaine Thanks for this detailed help. I am sorry I confused inter and intra. Shame! If I use either of the commands, the message is: Expected a keyword. If I use either of the menus, the message is: Invalid “restrict” argument. Expected “any” or “both” or”cross” or an atom specifier. I am using Chimerax 1.6.1. (College security system makes updating difficult but not impossible). Can you help? Thanks From Rosy From: Elaine Meng <meng@cgl.ucsf.edu> Date: Thursday, 5 December 2024 at 16:10 To: Rosaleen Calvert <rosy.calvert@kcl.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Intra-chain contacts [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Hi Rosy, Sounds like you want inter-chain (A <-->B), not intra-chain. There are several possible ways. One way is just command contacts /A restrict /B saveFile browse ...where "browse" means to open file browser dialog to specify file name/location interactively. Or you can just give the file name and location directly, for example: contacts /A restrict /B saveFile ~/Desktop/ABcontacts.txt There are lots of other command options if you want to change any of the detection criteria and display parameters, use command "help contacts" or see the copy of the manual page at our website: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fclashes.html&data=05%7C02%7Crosy.calvert%40kcl.ac.uk%7C1dc625d5689442f0217608dd15474cda%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638690118202880637%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=%2BmcIbYxFc6LojzZa21Fw%2BunLboOF02pF7zL5dQF5GqY%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>> You can do exactly the same thing with the Contacts tool, menu: Tools... Structure Analysis... Contacts, but you would need to first select one of the chains, e.g. A, and then choose the option in the Contacts tool: Limit by selection: between selection and atom spec... and enter "/B" in the box to the right of that, and check the "File" option like you said. <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fclashes.html&data=05%7C02%7Crosy.calvert%40kcl.ac.uk%7C1dc625d5689442f0217608dd15474cda%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638690118202912635%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=NNnVBkEvWkSvnnUsjN9RsB88oXlm85RQzS%2BOclUfwwo%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html>> You can also do it by first selecting chain A, then using menu: Select... Contacts, then choose Atomic tab and then use the same "Limit by selection" stuff as mentioned above. However, you would need to also click "Show Contacts tool" so that you could turn on the File option. <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fselectcontacts.html&data=05%7C02%7Crosy.calvert%40kcl.ac.uk%7C1dc625d5689442f0217608dd15474cda%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638690118202923312%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=6WTMRQUfQiP06RqVnrJvMCAapuwFrAxZv6SOcR4KZqA%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html>> The intermodel thing doesn't matter if you only have one model (if you only opened one structure file). If you have more than one model you may need to specify which one, for example command: contacts #1/A restrict #1/B [... other options...] ...and "#1/B" as the atomspec to limit in the dialogs mentioned above. 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 Dec 5, 2024, at 5:01 AM, Rosaleen Calvert via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi How do I get a text file of contacts A-B (NOT A-A or B-B). I have tried Show atoms Select Contacts Chain A on left. Chain B on right Uncheck intermodel Check file. Please help. Thanks. Rosy
Somehow your commands are wrong, but without seeing what command you tried, I can't tell you what is wrong. The only clue is what the message says, which is that what you put right after "restrict" is wrong. If using the GUI tools, you need to put something in the box, like "/B" for chain B in my example. Maybe you left it blank or just put B instead of /B Elaine
On Dec 10, 2024, at 4:38 AM, Rosaleen Calvert via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine Thanks for this detailed help. I am sorry I confused inter and intra. Shame! If I use either of the commands, the message is: Expected a keyword. If I use either of the menus, the message is: Invalid “restrict” argument. Expected “any” or “both” or”cross” or an atom specifier. I am using Chimerax 1.6.1. (College security system makes updating difficult but not impossible). Can you help? Thanks From Rosy From: Elaine Meng <meng@cgl.ucsf.edu> Date: Thursday, 5 December 2024 at 16:10 To: Rosaleen Calvert <rosy.calvert@kcl.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Intra-chain contacts [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important athttps://aka.ms/LearnAboutSenderIdentification ]
Hi Rosy, Sounds like you want inter-chain (A <-->B), not intra-chain.
There are several possible ways. One way is just command
contacts /A restrict /B saveFile browse
...where "browse" means to open file browser dialog to specify file name/location interactively. Or you can just give the file name and location directly, for example:
contacts /A restrict /B saveFile ~/Desktop/ABcontacts.txt
There are lots of other command options if you want to change any of the detection criteria and display parameters, use command "help contacts" or see the copy of the manual page at our website: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....>
You can do exactly the same thing with the Contacts tool, menu: Tools... Structure Analysis... Contacts, but you would need to first select one of the chains, e.g. A, and then choose the option in the Contacts tool: Limit by selection: between selection and atom spec... and enter "/B" in the box to the right of that, and check the "File" option like you said. <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....>
You can also do it by first selecting chain A, then using menu: Select... Contacts, then choose Atomic tab and then use the same "Limit by selection" stuff as mentioned above. However, you would need to also click "Show Contacts tool" so that you could turn on the File option. <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....>
The intermodel thing doesn't matter if you only have one model (if you only opened one structure file). If you have more than one model you may need to specify which one, for example command:
contacts #1/A restrict #1/B [... other options...]
...and "#1/B" as the atomspec to limit in the dialogs mentioned above.
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 Dec 5, 2024, at 5:01 AM, Rosaleen Calvert via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi How do I get a text file of contacts A-B (NOT A-A or B-B). I have tried Show atoms Select Contacts Chain A on left. Chain B on right Uncheck intermodel Check file. Please help. Thanks. Rosy
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/
Thanks. I had “/B”. Removed “”. It worked. Rosy From: Elaine Meng <meng@cgl.ucsf.edu> Date: Tuesday, 10 December 2024 at 16:47 To: Rosaleen Calvert <rosy.calvert@kcl.ac.uk> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Intra-chain contacts [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Somehow your commands are wrong, but without seeing what command you tried, I can't tell you what is wrong. The only clue is what the message says, which is that what you put right after "restrict" is wrong. If using the GUI tools, you need to put something in the box, like "/B" for chain B in my example. Maybe you left it blank or just put B instead of /B Elaine
On Dec 10, 2024, at 4:38 AM, Rosaleen Calvert via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine Thanks for this detailed help. I am sorry I confused inter and intra. Shame! If I use either of the commands, the message is: Expected a keyword. If I use either of the menus, the message is: Invalid “restrict” argument. Expected “any” or “both” or”cross” or an atom specifier. I am using Chimerax 1.6.1. (College security system makes updating difficult but not impossible). Can you help? Thanks From Rosy From: Elaine Meng <meng@cgl.ucsf.edu> Date: Thursday, 5 December 2024 at 16:10 To: Rosaleen Calvert <rosy.calvert@kcl.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Intra-chain contacts [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important athttps://aka.ms/LearnAboutSenderIdentification ]
Hi Rosy, Sounds like you want inter-chain (A <-->B), not intra-chain.
There are several possible ways. One way is just command
contacts /A restrict /B saveFile browse
...where "browse" means to open file browser dialog to specify file name/location interactively. Or you can just give the file name and location directly, for example:
contacts /A restrict /B saveFile ~/Desktop/ABcontacts.txt
There are lots of other command options if you want to change any of the detection criteria and display parameters, use command "help contacts" or see the copy of the manual page at our website: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fclashes.html&data=05%7C02%7Crosy.calvert%40kcl.ac.uk%7Cdfc57243a90143b29d7c08dd193a4d4e%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638694460394671330%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=aV0XfWcTaqXuKjxfKXlEpHU0Wd1NzHRblB47Anz5ig8%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>>
You can do exactly the same thing with the Contacts tool, menu: Tools... Structure Analysis... Contacts, but you would need to first select one of the chains, e.g. A, and then choose the option in the Contacts tool: Limit by selection: between selection and atom spec... and enter "/B" in the box to the right of that, and check the "File" option like you said. <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fclashes.html&data=05%7C02%7Crosy.calvert%40kcl.ac.uk%7Cdfc57243a90143b29d7c08dd193a4d4e%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638694460394687236%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=PFgCpz8R3aRUmAo9fE8yn7cwLOe%2FgIhWPcc9rgOG3OM%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html>>
You can also do it by first selecting chain A, then using menu: Select... Contacts, then choose Atomic tab and then use the same "Limit by selection" stuff as mentioned above. However, you would need to also click "Show Contacts tool" so that you could turn on the File option. <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fselectcontacts.html&data=05%7C02%7Crosy.calvert%40kcl.ac.uk%7Cdfc57243a90143b29d7c08dd193a4d4e%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638694460394696470%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=0Wvz4K7RAu0162M85fKhi9hErlddBEDFoxpoq0WRFUg%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html>>
The intermodel thing doesn't matter if you only have one model (if you only opened one structure file). If you have more than one model you may need to specify which one, for example command:
contacts #1/A restrict #1/B [... other options...]
...and "#1/B" as the atomspec to limit in the dialogs mentioned above.
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 Dec 5, 2024, at 5:01 AM, Rosaleen Calvert via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi How do I get a text file of contacts A-B (NOT A-A or B-B). I have tried Show atoms Select Contacts Chain A on left. Chain B on right Uncheck intermodel Check file. Please help. Thanks. Rosy
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimerax-users%40cgl.ucsf.edu%2F&data=05%7C02%7Crosy.calvert%40kcl.ac.uk%7Cdfc57243a90143b29d7c08dd193a4d4e%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638694460394705987%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=lM9tegXup4rgnGm8nIOrLk4nHAkwiva7X0w%2BbeOY0Qs%3D&reserved=0<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/>
participants (2)
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Elaine Meng -
Rosaleen Calvert