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

[Jose M. de la R. T. <del...@gm...>]

Great! There are a couple bugfixes algo coming in 3.0.0b4.

Have a nice weekend,
Jose Miguel


On Fri, Oct 9, 2020, 3:55 PM Lugmayr, Wolfgang <w.l...@uk...> wrote:

> dear all,
>
> its fixed with scipion-em-relion 3.0.0b3 plugin version.
>
> thanks,
> wolfgang
>
>
> ------------------------------
> *From: *"Lugmayr, Wolfgang" <w.l...@uk...>
> *To: *"Mailing list for Scipion users" <
> sci...@li...>
> *Sent: *Friday, 9 October, 2020 15:45:09
> *Subject: *Re: [scipion-users] scipion3 - relion protocol viewer -
> chimerax script problem
>
> 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 Scipion <http://scipion.i2pc.es> team*
>
>
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