[chimerax-users] Move atoms

[Elaine Meng]

> On Feb 21, 2021, at 11:40 PM, Ruben Meerman <rubenmeerman at me.com> wrote:
> 
> I am trying to use the move command to move all the atoms of a single DNA nucleotide, but the whole model moves:
> 
> move x 3 5 model #1 atoms #1/a:44
> 
> The PDB model I’m testing the command on is 6BY7 (a DNA nano barrel) 
> 
> Am I doing something wrong, or just dopey?
> Kind regards,
> Ruben
> 
> ps my ultimate aim is to a set of commands to untwist and unzip DNA using the move and roll commands… not sure if that’s a bit too ambitious

Hi Ruben,
I'm CC-ing the list, but yes in general please do send the question to the list in the first place unless it includes data that you have to keep private.

The "model #1" option says to move all of model #1. Omit that if you only want to move the atoms. Also it looks like you have an extra number in there (3 or the 5).  Maybe something like:

move x 5 atoms #1/A:44

"move" manual page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html>

Structure 6by7 does not have a chain A, so you'd need a different command than the above for that specific structure.

However, it sounds very difficult to untwist DNA using rigid-body movements of sets of atoms. Here are a couple of other ideas, but they are just ideas (don't know whether either one would work well) and would also take some effort to try.

(1) use "torsion" command instead
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html>

(2) build a separate completely untwisted version (not available in ChimeraX, maybe via other programs, or in ChimeraX by using "torsion") and then use "morph" to morph between the twisted and untwisted
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco