Dear ChimeraX Team, my name is Mirko Ploesser, I am a Phd student in the Frankgakis group at the BMLS (Buchmann Institue for Molecular Life Sciences) in Frankfurt (Germany) and currently working on a ChimeraX bundle. Thanks to your detailed tutorial on how to develop bundles, I have already made a good progeress in doing so. Currently, however, I am stuck with a problem that I hanve't found a solution to yet. I would be very thankful if you could give me advice on how to progress. The problem is described as follows: I click a set of markers in a volume (tomogram as an EM file) and save the corresponding positions. At those positions I want to load different and smaller volumes (also EM Files). The information about those smaller volumes - position and rotation - I have saved in a different file (a motivelist in also an EM format). Now I am stuck with the problem on how to update the rotation angles when I use the tool "Rotate model" using the right mouse. I know that the corresponding rotation matrix is printed in the log. Is there any way that I can use the information given to the log in my bundle code? Also, since we already have a working version of the bundle in Chimera, I found the module "openModel" very useful. Unfortunately I haven't been able to find an equivalent module in ChimeraX. So I guess there is a different approach to this used in ChimeraX. I would be very happy if you could also help me out in this regard. Thank you very much in advance for your time and effort. I am looking forward to hearing from you soon. Best, Mirko Ploesser
Hi Mirko! Others will need to respond on the bundle/programming issues, but here's a brief note about applying rotations: Probably you wouldn't be using the mouse mode. There is a ChimeraX command "view matrix" that can report and apply matrices to models: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix> Alternatively, there is a ChimeraX positions file format that you can save or open, and opening it applies the matrices: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/positions.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 24, 2021, at 11:35 PM, Mirko Plößer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team,
my name is Mirko Ploesser, I am a Phd student in the Frankgakis group at the BMLS (Buchmann Institue for Molecular Life Sciences) in Frankfurt (Germany) and currently working on a ChimeraX bundle. Thanks to your detailed tutorial on how to develop bundles, I have already made a good progeress in doing so. Currently, however, I am stuck with a problem that I hanve't found a solution to yet. I would be very thankful if you could give me advice on how to progress.
The problem is described as follows: I click a set of markers in a volume (tomogram as an EM file) and save the corresponding positions. At those positions I want to load different and smaller volumes (also EM Files). The information about those smaller volumes - position and rotation - I have saved in a different file (a motivelist in also an EM format). Now I am stuck with the problem on how to update the rotation angles when I use the tool "Rotate model" using the right mouse. I know that the corresponding rotation matrix is printed in the log. Is there any way that I can use the information given to the log in my bundle code?
Also, since we already have a working version of the bundle in Chimera, I found the module "openModel" very useful. Unfortunately I haven't been able to find an equivalent module in ChimeraX. So I guess there is a different approach to this used in ChimeraX. I would be very happy if you could also help me out in this regard.
Thank you very much in advance for your time and effort. I am looking forward to hearing from you soon.
Best, Mirko Ploesser _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Dear Elaine, than you very much for your reply! I think especially the ChimeraX positions file, which I did not know about before, will be of help. Thanks a lot for your input. Best, Mirko Quoting Elaine Meng <meng@cgl.ucsf.edu>:
Hi Mirko! Others will need to respond on the bundle/programming issues, but here's a brief note about applying rotations:
Probably you wouldn't be using the mouse mode. There is a ChimeraX command "view matrix" that can report and apply matrices to models: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix>
Alternatively, there is a ChimeraX positions file format that you can save or open, and opening it applies the matrices: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/positions.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 24, 2021, at 11:35 PM, Mirko Plößer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team,
my name is Mirko Ploesser, I am a Phd student in the Frankgakis group at the BMLS (Buchmann Institue for Molecular Life Sciences) in Frankfurt (Germany) and currently working on a ChimeraX bundle. Thanks to your detailed tutorial on how to develop bundles, I have already made a good progeress in doing so. Currently, however, I am stuck with a problem that I hanve't found a solution to yet. I would be very thankful if you could give me advice on how to progress.
The problem is described as follows: I click a set of markers in a volume (tomogram as an EM file) and save the corresponding positions. At those positions I want to load different and smaller volumes (also EM Files). The information about those smaller volumes - position and rotation - I have saved in a different file (a motivelist in also an EM format). Now I am stuck with the problem on how to update the rotation angles when I use the tool "Rotate model" using the right mouse. I know that the corresponding rotation matrix is printed in the log. Is there any way that I can use the information given to the log in my bundle code?
Also, since we already have a working version of the bundle in Chimera, I found the module "openModel" very useful. Unfortunately I haven't been able to find an equivalent module in ChimeraX. So I guess there is a different approach to this used in ChimeraX. I would be very happy if you could also help me out in this regard.
Thank you very much in advance for your time and effort. I am looking forward to hearing from you soon.
Best, Mirko Ploesser _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Mirko, I don't totally understand the details of what you need, but here's some info. If you rotate a selected model using the "Rotate model" mouse mode then its position matrix changes. First Python to get the list of selected models is session.selection.models() If it is a volume (ie map) model that got rotated then I could find the selected volumes like this from chimerax.map import Volume volumes = [v for v in session.selection.models() if isinstance(v, Volume)] And if I wanted to print their 3x4 position matrices (first 3 columns are the rotation, 4th column is a translation done after rotation) for v in volumes: print (v.position.matrix) Now I don't know what you mean by "update the rotation angles". Are you trying to record Euler angles? If so you could get the Euler angles in z-x-z convention like this from chimerax.geometry.matrix import euler_angles for v in volumes: alpha, beta, gamma = euler_angles(v.position.matrix) # Angles in degrees print ('Volume %s Euler angles %.2f %.2f %.2f degrees (z-x-z convention)' % (v.name_with_id(), alpha, beta, gamma) In Chimera the openModels object holds the list of models. In ChimeraX this is session.models. For example to show the names of all models: for m in session.models.list(): print ('#' + m.id_string + ' ' + m.name) The programmer documentation https://www.cgl.ucsf.edu/chimerax/docs/devel/index.html <https://www.cgl.ucsf.edu/chimerax/docs/devel/index.html> has info about the various ChimeraX functions, for instance for models https://www.cgl.ucsf.edu/chimerax/docs/devel/core/models.html <https://www.cgl.ucsf.edu/chimerax/docs/devel/core/models.html> There is some example Python code at the ChimeraX recipes web site that can be useful. https://rbvi.github.io/chimerax-recipes/ Back in March 2021 I was talking with Matthias Vorlander to place a subtomogram average at positions in a tomogram given by a Relion STAR file. https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-March/002093.html I've attached the code we came up with. Maybe that will be useful to you. I am happy to answer more programming questions. Keep sending them to this list unless you want to send private data in which case you can send directly to me. Tom
On Aug 24, 2021, at 11:35 PM, Mirko Plößer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team,
my name is Mirko Ploesser, I am a Phd student in the Frankgakis group at the BMLS (Buchmann Institue for Molecular Life Sciences) in Frankfurt (Germany) and currently working on a ChimeraX bundle. Thanks to your detailed tutorial on how to develop bundles, I have already made a good progeress in doing so. Currently, however, I am stuck with a problem that I hanve't found a solution to yet. I would be very thankful if you could give me advice on how to progress.
The problem is described as follows: I click a set of markers in a volume (tomogram as an EM file) and save the corresponding positions. At those positions I want to load different and smaller volumes (also EM Files). The information about those smaller volumes - position and rotation - I have saved in a different file (a motivelist in also an EM format). Now I am stuck with the problem on how to update the rotation angles when I use the tool "Rotate model" using the right mouse. I know that the corresponding rotation matrix is printed in the log. Is there any way that I can use the information given to the log in my bundle code?
Also, since we already have a working version of the bundle in Chimera, I found the module "openModel" very useful. Unfortunately I haven't been able to find an equivalent module in ChimeraX. So I guess there is a different approach to this used in ChimeraX. I would be very happy if you could also help me out in this regard.
Thank you very much in advance for your time and effort. I am looking forward to hearing from you soon.
Best, Mirko Ploesser _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Elaine Meng -
Mirko Plößer -
Tom Goddard