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
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@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@cgl.ucsf.edu] Sent: Friday, October 23, 2020 5:56 PM To: Jeschke Gunnar Cc: chimerax-users@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@phys.chem.ethz.ch<mailto:gunnar.jeschke@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> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Well, it's a hack but if you know the starting coordinates of the atom you can use three "move" commands (one per axis) to position it. If you don't know the coordinates, you can use the setattr trick you discovered to set the coordinates to (0,0,0) and then use the move commands. --Eric
On Oct 24, 2020, at 1:08 AM, Jeschke Gunnar <gunnar.jeschke@phys.chem.ethz.ch> wrote:
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 <http://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 <http://www.epr.ethz.ch/> ________________________________________ From: Eric Pettersen [pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>] Sent: Friday, October 23, 2020 5:56 PM To: Jeschke Gunnar Cc: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@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@phys.chem.ethz.ch <mailto:gunnar.jeschke@phys.chem.ethz.ch><mailto:gunnar.jeschke@phys.chem.ethz.ch <mailto:gunnar.jeschke@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/><http://www.epr.ethz.ch <http://www.epr.ethz.ch/>> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
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I too had assumed it would be possible to use setattr and the REST interface in the way Gunnar asked about, with an XYZ triplet - for generic 3D scatterplots. The workaround you described will certainly work. I just wanted to mention that doing this directly might indeed be useful. The REST interface opens so many creative options when coming from other languages, e.g. from R. Cheers, Boris -- Boris Steipe MD, PhD Associate Professor, Department of Biochemistry and Department of Molecular Genetics Temerty Faculty of Medicine University of Toronto
On 2020-10-27, at 02:52, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
EXTERNAL EMAIL: Treat content with extra caution. Well, it's a hack but if you know the starting coordinates of the atom you can use three "move" commands (one per axis) to position it. If you don't know the coordinates, you can use the setattr trick you discovered to set the coordinates to (0,0,0) and then use the move commands.
--Eric
On Oct 24, 2020, at 1:08 AM, Jeschke Gunnar <gunnar.jeschke@phys.chem.ethz.ch> wrote:
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@cgl.ucsf.edu] Sent: Friday, October 23, 2020 5:56 PM To: Jeschke Gunnar Cc: chimerax-users@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@phys.chem.ethz.ch<mailto:gunnar.jeschke@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> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
For making a scatter plot in 3D from atoms you can use the ChimeraX marker command. It places sphere markers which in fact are just atoms mark #3 position 10,2.8,4 radius 1.5 color yellow Also since markers are just atoms, the "marker change" command can change the position of an atom mark change #1/B:9@CA position -2.6,4.1,3 Docs for the marker command https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html> Tom
On Oct 26, 2020, at 10:30 AM, Boris Steipe <boris.steipe@utoronto.ca> wrote:
I too had assumed it would be possible to use setattr and the REST interface in the way Gunnar asked about, with an XYZ triplet - for generic 3D scatterplots. The workaround you described will certainly work. I just wanted to mention that doing this directly might indeed be useful. The REST interface opens so many creative options when coming from other languages, e.g. from R.
Cheers, Boris
-- Boris Steipe MD, PhD
Associate Professor, Department of Biochemistry and Department of Molecular Genetics Temerty Faculty of Medicine University of Toronto
On 2020-10-27, at 02:52, Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote:
EXTERNAL EMAIL: Treat content with extra caution. Well, it's a hack but if you know the starting coordinates of the atom you can use three "move" commands (one per axis) to position it. If you don't know the coordinates, you can use the setattr trick you discovered to set the coordinates to (0,0,0) and then use the move commands.
--Eric
On Oct 24, 2020, at 1:08 AM, Jeschke Gunnar <gunnar.jeschke@phys.chem.ethz.ch <mailto:gunnar.jeschke@phys.chem.ethz.ch>> wrote:
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 <http://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 <http://www.epr.ethz.ch/> ________________________________________ From: Eric Pettersen [pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>] Sent: Friday, October 23, 2020 5:56 PM To: Jeschke Gunnar Cc: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@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@phys.chem.ethz.ch <mailto:gunnar.jeschke@phys.chem.ethz.ch><mailto:gunnar.jeschke@phys.chem.ethz.ch <mailto:gunnar.jeschke@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/><http://www.epr.ethz.ch <http://www.epr.ethz.ch/>> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
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Dear Tom,
mark change #1/B:9@CA position -2.6,4.1,3
This is what I finally implemented. Thanks a lot and 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: Tom Goddard [goddard@sonic.net] Sent: Monday, October 26, 2020 7:00 PM To: Boris Steipe; Jeschke Gunnar Cc: chimerax-users Subject: Re: [chimerax-users] Set atom coordinates by command? For making a scatter plot in 3D from atoms you can use the ChimeraX marker command. It places sphere markers which in fact are just atoms mark #3 position 10,2.8,4 radius 1.5 color yellow Also since markers are just atoms, the "marker change" command can change the position of an atom mark change #1/B:9@CA position -2.6,4.1,3 Docs for the marker command https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html Tom On Oct 26, 2020, at 10:30 AM, Boris Steipe <boris.steipe@utoronto.ca<mailto:boris.steipe@utoronto.ca>> wrote: I too had assumed it would be possible to use setattr and the REST interface in the way Gunnar asked about, with an XYZ triplet - for generic 3D scatterplots. The workaround you described will certainly work. I just wanted to mention that doing this directly might indeed be useful. The REST interface opens so many creative options when coming from other languages, e.g. from R. Cheers, Boris -- Boris Steipe MD, PhD Associate Professor, Department of Biochemistry and Department of Molecular Genetics Temerty Faculty of Medicine University of Toronto On 2020-10-27, at 02:52, Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> wrote: EXTERNAL EMAIL: Treat content with extra caution. Well, it's a hack but if you know the starting coordinates of the atom you can use three "move" commands (one per axis) to position it. If you don't know the coordinates, you can use the setattr trick you discovered to set the coordinates to (0,0,0) and then use the move commands. --Eric On Oct 24, 2020, at 1:08 AM, Jeschke Gunnar <gunnar.jeschke@phys.chem.ethz.ch<mailto:gunnar.jeschke@phys.chem.ethz.ch>> wrote: 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<http://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<http://www.epr.ethz.ch/> ________________________________________ From: Eric Pettersen [pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>] Sent: Friday, October 23, 2020 5:56 PM To: Jeschke Gunnar Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@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@phys.chem.ethz.ch<mailto:gunnar.jeschke@phys.chem.ethz.ch><mailto:gunnar.jeschke@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/><http://www.epr.ethz.ch<http://www.epr.ethz.ch/>> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (4)
-
Boris Steipe -
Eric Pettersen -
Jeschke Gunnar -
Tom Goddard