[Chimera-users] Writing data to a text file

[Prathvi Singh]

I got it. Thanks Elaine.

On Tue, Nov 9, 2021 at 7:21 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Sorry, no.  It is actually quite difficult to implement undo, or so I'm
> told (I'm not the one doing it).  Chimera has an "Undo Move" tool but
> that's pretty much it, and we are not actively developing Chimera to add
> features any more.
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/undomove/undomove.html
> >
>
> Our development focus is now on ChimeraX.  The ChimeraX undo doesn't
> include everything, but we tried to include many common actions.  Glad you
> like it!
>
> ChimeraX undo:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/undo.html>
>
> ChimeraX short list of advantages over Chimera:
> <https://rbvi.ucsf.edu/chimerax/docs/user/advantages.html>
>
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Nov 8, 2021, at 5:41 PM, Prathvi Singh via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > 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
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription:
> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>

-- 
Prathvi Singh,
Research Fellow,
Department of Biological Sciences & Bioengineering,
Indian Institute of Technology, Kanpur-208016
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