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