Hi Paul, The "Clashes" or "Contacts" tool (or "clashes" or "contacts" commands) all have an option to write output to a file or to the Log. I believe it is in order of greatest to least VDW overlap, but there is a center-to-center distance column as well that you could then sort by (e.g. if you wrote an output file). These also have an option to use center-to-center distance as the main criterion and ignore VDW overlap, and that would give results in order of distance. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> No, the above do not say what kind of interaction is involved. You would have to use your own chemical knowledge of atom types to tell (and also distinguish them from overly close, unfavorable "clashes" ... although that is what the VDW overlap value is meant to tell you in the first place). If you use "H-Bonds" tool (command "hbonds") there are similar output options, except all of the lines are H-bonds. They also have an option to find only salt bridges (H-bonds that are also salt bridges). <https://rbvi.ucsf.edu/chimerax/docs/user/tools/hbonds.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html> For start/end, you can use the words "start" and "end" as explained in the atomspec documentation: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#lists> 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 Nov 25, 2024, at 1:19 AM, Paul Miller via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi
Is there a way by command line to generate a list of residue to residue (or atom to atom) distances ranked by closest to furthest, for say, all residues within 4A of each other at an interface between two protein chains? Can it also state the type of interaction, e.g. salt bridge, H-bond, vdW?
Also, completely separately, is there a way by command line to select the first and last residue in a chain (without having to find their number)?
No worries if not. Thanks so much!
Cheers, Paul