[chimerax-users] Move atoms

[Ruben Meerman]

Hi Elaine,

Yes, that helped immensely! I managed to untwist one strand of a 10bp DNA model using a combination of “torsion” and “angle”. I then opened the same model and the two did morph but not with an untwisting motion. 

There’s no option to make untwisted DNA with a straight backbone in Avogadro so I’ll experiment with “angle”, “torsion” and “move”. I will let you know how I go.

Many thanks for your advice,

Ruben

> On 23 Feb 2021, at 2:37 am, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
>> 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
> 
> 
> 
> 

______________________
Ruben Meerman
M: 0414 680 271
E: rubenmeerman at me.com



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