Re: [chimerax-users] Move atoms
On Feb 21, 2021, at 11:40 PM, Ruben Meerman rubenmeerman@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
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@cgl.ucsf.edu wrote:
On Feb 21, 2021, at 11:40 PM, Ruben Meerman rubenmeerman@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@me.com
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