[chimerax-users] Set atom coordinates by command?
Jeschke Gunnar
gunnar.jeschke at phys.chem.ethz.ch
Sat Oct 24 01:08:41 PDT 2020
Hi Eric,
thanks. No problem at all.
I will eventually use the Python shell, but for the moment I am content with communicating via REST, which works just fine for visualization purposes.
I justed wanted to know what I can and cannot implement in this interface.
Kind regards
Gunnar
---
It's about time: The Great Barrington Declaration
gbdeclaration.org
Prof. Dr. Gunnar Jeschke
ETH Zurich
Department of Chemistry and Applied Biosciences
Vladimir-Prelog-Weg 2
CH-8093 Zurich Switzerland
www.epr.ethz.ch
________________________________________
From: Eric Pettersen [pett at cgl.ucsf.edu]
Sent: Friday, October 23, 2020 5:56 PM
To: Jeschke Gunnar
Cc: chimerax-users at cgl.ucsf.edu
Subject: Re: [chimerax-users] Set atom coordinates by command?
Hi Gunnar,
The setattr command can't do this. It would not be too hard to add it to setattr, but it doesn't seem to be something anyone would commonly want to do, though I'm willing to listen to arguments otherwise.
This is pretty easy to do in ChimeraX's Python shell though (Tools→General→Shell). The following code (typed/pasted) to the shell would set all selected atoms' coordinates to 1,2,3:
from chimerax.atomic import selected_atoms as sel_atoms
for a in sel_atoms(session):
a.coord = (1, 2, 3)
If you're not familiar with Python, indentation is significant, so that last line needs to be indented as shown.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
On Oct 23, 2020, at 12:52 AM, Jeschke Gunnar <gunnar.jeschke at phys.chem.ethz.ch<mailto:gunnar.jeschke at phys.chem.ethz.ch>> wrote:
Hi all,
is there a way to set atom coordinates by a command?
setattr spec atoms coord value
appears to accept only one double argument and sets x, y, and z to this number. Neither space-separated nor comma-separate lists of three values appear to work.
Kind regards
Gunnar
---
Prof. Dr. Gunnar Jeschke
ETH Zurich
Department of Chemistry and Applied Biosciences
Vladimir-Prelog-Weg 2
CH-8093 Zurich Switzerland
www.epr.ethz.ch<http://www.epr.ethz.ch>
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