[chimerax-users] ChimeraX Bundle

[Elaine Meng]

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 at 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
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