[Chimera-users] Writing data to a text file

[Elaine Meng]

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
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