Re: [scipion-users] scipion3 - relion protocol viewer - chimerax script problem

[Pablo C. <pc...@cn...>]

Hi Wolfgang,

I've run the tests:

scipion3 tests relion.tests.test_protocols_relion.TestRelionClassify3D

And got a proper output:

pablo@youyou:~/desarrollo/scipion-em-relion$ cat 
~/ScipionUserData/projects/TestRelionClassify3D/Runs/000294_ProtRelionClassify3D/extra/chimera_volumes.cxc 

open relion_it008_class001.mrc
open relion_it008_class002.mrc
open relion_it008_class003.mrc
tile


I'm guessing....did you actually get any volume?


On 9/10/20 11:17, Lugmayr, Wolfgang wrote:
> hi,
>
> i run relion class3d and run into the following problem when looking at the volume that the chimerax cxc script only contains the word "tile":
>
> $ cat Runs/003565_ProtRelionClassify3D/tmp/chimera_angular_distribution.cxc
> open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/tmp/axis.bild
> open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/tmp/spheres.bild
> cofr 0,0,0
> open /beegfs/cssb/user/lugmayr/TestSets/Scipion3_TestSuite/Runs/003565_ProtRelionClassify3D/extra/relion_it025_class001.mrc
> volume #3 voxelSize 0.87
> volume #3 origin -104.4,-104.4,-104.4
>
> $ cat Runs/003565_ProtRelionClassify3D/extra/chimera_volumes.cxc
> tile
>
> settings used:
> 3D classes to visualize: -> selection -> Classes used: 1
> Display volume with: chimera
>
> pressing the eye button calls:
> ChimeraX Runs/003565_ProtRelionClassify3D/extra/chimera_volumes.cxc
> with no other arguments so i assume the open statements are overwritten
>
> the same behaviour is also when looking at the initial model, so i assume its the same code statement.
>
> cheers,
> wolfgang
>
> p.s. fyi: i am working on a virtual desktop on the cluster, so i had to replace ChimeraX by a script
> vglrun +xcb /.../ChimeraX.orig $*
> to overcome the usual ChimeraX problem:
> WARNING: WebEngineContext? used before QtWebEngine::initialize() or OpenGL context creation failed.
> ERROR: Could not create OpenGL context
>
>
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*