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

[Lugmayr, W. <w.l...@uk...>]

hi pablo, 

yes i got my volumes and can view the results with chimera and the chimera_angular_distribution.cxc script. 
the other views like slices, show in scipion etc. give reasonable views on my original data. 

the test produces for me in the scipion gui also a "tile" only file. 
see attached screenshot. 
it does not matter if i choose class 1 or all. 
the behaviour is the same. 

the line "runnning ChimeraX" comes from my vglrun wrapper but does not modify the cxc file. 

cheers, 
wolfgang 




From: "Pablo Conesa" <pc...@cn...> 
To: "Mailing list for Scipion users" <sci...@li...> 
Sent: Friday, 9 October, 2020 14:01:57 
Subject: Re: [scipion-users] scipion3 - relion protocol viewer - chimerax script problem 



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 [ http://scipion.i2pc.es/ | Scipion ] team 


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