[Chimera-users] Writing data to a text file

Prathvi Singh prathvi at iitk.ac.in
Mon Nov 8 17:41:30 PST 2021

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 at 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/findclash.html
> >
> 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 at 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
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