Dear Amita, (1) The AlphaFold calculation is on Google Colab which has limitations, and it may or may not be possible to run the calculation that you are trying to run. It depends on your specific data, and what the reason was for termination. See the help for the possible problems and possible solutions: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#caveats> (2) There is an option to save a file in the H-Bonds tool (and also the hbonds command). H-Bonds tool has "Write information to" option, you can turn this on and choose file, see the bottom of the help page: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/hbonds.html> "hbonds" command has "saveFile" option, see the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html#saveFile> I don't know which tool you are using to find protein-protein interactions. If you are using Contacts, just like H-Bonds, it has a "Write information to" option, and the "contacts" command has a "saveFile" option. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html#saveFile> Or, if you are using ChimeraX menu: Select... Contacts, after you make the selection <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> ... then you can write a list of the selected atoms to a file using command "info atoms sel" or "info residues sel" if you also use the "saveFile" option in that command, for example on my Mac I can use command: info residues sel saveFile ~/Desktop/residue-list See the help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#saveFile> 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 Apr 2, 2024, at 12:58 PM, Amita Mohan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I would appreciate if you please answer the following questions:
1. I am using chimeraX, and I have a trouble getting results from Alphafold. The Google Colab keep on termination without saving results. Could you please help?
2. I am using hydrogen bond tool, how can I save all the H-bonds in the protein as file containing all the information for the paired residues involved in the H bond. Similarly, I also would like to save the information of residues involved in the protein-protein interactions.
I hope to hear from you.
Best, Amita Department of Biology University of Pennsylvania