[chimera-dev] Retrieving model_id / model_name via API

Lars Hangartner lhangart at scripps.edu
Thu Mar 7 16:06:45 PST 2019


Yup, that took care of it, it works now.

Thanks Tom!

Lars


On Mar 7, 2019, at 3:12 PM, Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>> wrote:

Oops.  Should be

v.new_region(ijk_step = (1,1,1), adjust_step = False)

Chimera automatically adjust the step size to stay within a maximum total number of voxels.  The adjust_step = False means not to do that automatic changing of the specified step.

Tom


On Mar 7, 2019, at 2:57 PM, Lars Hangartner <lhangart at scripps.edu<mailto:lhangart at scripps.edu>> wrote:

Hi Tom.

Thanks for the reply. Unfortunately, this did not work. My implementation was as follows and did not change anything.
Best,
Lars

for vol in openModels.list(modelTypes=[Volume]):
    vol.new_region(ijk_step = (1,1,1))



On Mar 7, 2019, at 1:07 PM, Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>> wrote:

To set the step of a Volume model v in Chimera in Python code

v.new_region(ijk_step = (1,1,1))

  Tom


On Mar 6, 2019, at 8:42 PM, Lars Hangartner <lhangart at scripps.edu<mailto:lhangart at scripps.edu>> wrote:

Hi Eric,

Thanks for the swift response, worked like a charm. May I also ask how to set the ’step’ property value from the volume viewer GUI pop-up from a script?

Thanks,

Lars

On Mar 6, 2019, at 3:40 PM, Eric Pettersen <pett at cgl.ucsf.edu<mailto:pett at cgl.ucsf.edu>> wrote:

Hi Lars,
The model attributes for the ID are ‘id’/‘subid’ for the parts before and after any ‘.’ respectively, and the ‘name’ attribute has the model name.  You would loop through all volume models with something like:

from chimera import openModels
from VolumeViewer import Volume
for vol in openModels.list(modelTypes=[Volume]):
print “%d.%d %s” % (vol.id<http://vol.id/>, vol.subid, vol.name)

We realize the programmer documentation isn’t great.  What little we have you can find here: https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html .  One of our objectives for ChimeraX is much better programmer documentation.

—Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Mar 6, 2019, at 10:40 AM, Lars Hangartner <lhangart at scripps.edu<mailto:lhangart at scripps.edu>> wrote:

Hi guys,

I am desperately looking to get the model_id / model name from all open volume objects. I have tried openModel.list()[0].model_id  in many iterations but no success… I would like to iterate through models and identify the resampled ones.

Can anybody help?

Thanks,

Lars


P.S: API documentation would really be helpful.



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