Thanks Elaine for the help. I checked out ChimeraX & it is definitely much more user-friendly. The presence of the reply log at the right side really helps keep track of the actions one is performing and THANKS A LOT for the undo feature. I really miss it in Chimera. Still, I wonder if there is a way or a plugin to incorporate the "undo" command in chimera... On Mon, Nov 8, 2021 at 9:35 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Prathvi, You can get all-by-all distances written to a file or the Reply Log by using Find Clashes/Contacts or the clashes command, by defining residue-A as the first set of atoms, residue-B as the second set of atoms, and and using a large negative cutoff value that will just get everything. For example, if it's residue 10 in chain A of model 0 versus residue 50 in chain B of model 1, the command to send info to the Log could be something like
findclash #0:10.A test #1:50.B overlap -1000 log true
(and/or use the saveFile option to save to file)
Find Clashes/Contacts tool < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findcla...
findclash command and its options <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
ChimeraX (our newer program) also has a tool and command to do this same thing, if you're interested.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 8, 2021, at 3:39 AM, Prathvi Singh via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hi, Suppose I want to find the distance between all atoms of residue-A and residue-B & write the distances to a file. Is it possible to do so in a meaningful way?
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016