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delarosatrevin / scipion

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM)
http://scipion.cnb.csic.es
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New protocls of Relion 3.0 can't be detected (EXCEPT MULTIBODY) #47

Closed vabrishami closed 5 years ago

vabrishami commented 5 years ago

Describe the bug

The new protocols of Relion 3.0 such as Bayesian Polishing do not appear in the tree viewer and even I can not find them using Search Protocol. Multibody refinement is the only protocol which appears in the tree viewer.

To Reproduce I followed the steps of "Testing Relion 3 in Scipion" and made a soft link to Relion 3.0 that we currently use, and after installing, I just run the Scipion.

Expected behavior To see the new protocols of Relion 3.0 in the tree viewer or to search for them using Search Protocol.

Screenshots image

Desktop

delarosatrevin commented 5 years ago

Hi @vabrishami , thanks for reporting. Have you modified the user configuration file to point to Relion 3 as well?

vabrishami commented 5 years ago

Hi @delarosatrevin

So I made a soft link in software/em which points to my already installed Relion 3.0 and then changed Relion home to:

RELION_HOME = %(EM_ROOT)s/relion-3.0

delarosatrevin commented 5 years ago

Ok, then it is correct...the protocols should appear at least in the Search dialog. I will take a look.

andreanans commented 5 years ago

Hi, I just ran the relion 3.0 test (worked fine), however I cannot search for any of the new relion-3.0 protocols. I double-checked that RELION_HOME points to relion-3.0.

delarosatrevin commented 5 years ago

Hi Andrea, yesterday I found same issue during a course in Helsinki and I know how to fix it. I will get back to you later.

On Wed, Mar 6, 2019, 1:26 PM andreanans notifications@github.com wrote:

Hi, I just ran the relion 3.0 test (worked fine), however I cannot search for any of the new relion-3.0 protocols. I double-checked that RELION_HOME points to relion-3.0.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/delarosatrevin/scipion/issues/47#issuecomment-470072641, or mute the thread https://github.com/notifications/unsubscribe-auth/AIDPWHdmeCNlVLXck8hqiS71yDrtBbz0ks5vT6X5gaJpZM4ab8Lk .

delarosatrevin commented 5 years ago

Hi @andreanans,

The issue with Relion3 protocols not showing up, was due to the matching of relion version. There was a bug that was wrongly reporting version '2.1' despite having Relion 3 in the configuration files.

I have submitted the fix, along with other updates/fixes to my branch. You you can update with git pull and after that, you should be able to find the relion protocols.

@vabrishami you could also undo the temporary fix there and update with latest changes.

I'm closing this issue, please let me know if it is working or no.

andreanans commented 5 years ago

Yep, I can see all of the protocols. Thanks! Will give it a try soon.. One quick question, if I want to do Bayesian polishing at this point do I have to use Relion's implementation of motioncor2? Is there a plan to write out the metadata star files after running the GPU version?

delarosatrevin commented 5 years ago

This is the beauty of Scipion...you can use any motion correction method that you want (e.g motioncor2, unblur, relion, etc) and later you can use the Bayesian Polishing...in the later, I create the proper .star files expected by Relion, taking the info of the shifts stored with the input movies.