Topaz training, coordinates in particle.star not recognized #96
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I am using Topaz inside of RELION. I used RELION's manual and autopicking routines to select several thousand particles. Those were whittled down using 2D classification and selecting only good classes. Now I want to use the particles from these good classes to train Topaz. But when I read in the particles.star file, I get an error "no training particles specified." What am I doing wrong? One more question: RELION allows one to combine micrographs taken at different pixel sizes. Can I use a combined set within Topaz for training and picking? I assumed not and was running that way when I encountered the problem in the above paragraph. David |
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Replies: 4 comments 1 reply
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Further information: I am using RELION 3.1.1 and Topaz 0.2.5. |
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Can you share a copy of the particles.star file? It isn't clear exactly what the problem is, but that seems like the place to start. |
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Tristan,
15 MB file wouldn’t go. Here is a compressed (via “tar -zcvf DMB-particles.star.tgz particles.star”) file. Only 2 MB.
David
From: David Michael Belnap ***@***.***>
Date: Thursday, March 25, 2021 at 8:35 AM
To: tbepler/topaz ***@***.***>, tbepler/topaz ***@***.***>
Cc: Author ***@***.***>
Subject: Re: [tbepler/topaz] Topaz training, coordinates in particle.star not recognized (#96)
Thank you. I’ve attached the particles.star file.
David
From: Tristan Bepler ***@***.***>
Reply-To: tbepler/topaz ***@***.***>
Date: Thursday, March 25, 2021 at 4:53 AM
To: tbepler/topaz ***@***.***>
Cc: David Michael Belnap ***@***.***>, Author ***@***.***>
Subject: Re: [tbepler/topaz] Topaz training, coordinates in particle.star not recognized (#96)
Can you share a copy of the particles.star file? It isn't clear exactly what the problem is, but that seems like the place to start.
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I found the problem. I entered the particles.star file under the "input coordinates" line in the External RELION job page. If I enter instead under the "input particles" line, then the process worked. I erroneously assumed I needed to submit under the coordinates line because I wanted the coordinate data. Apparently the RELION routine extracts the coordinates from the particles file for the Topaz job. Thank you, David |
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Great, glad you found the solution! |
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I found the problem. I entered the particles.star file under the "input coordinates" line in the External RELION job page. If I enter instead under the "input particles" line, then the process worked. I erroneously assumed I needed to submit under the coordinates line because I wanted the coordinate data. Apparently the RELION routine extracts the coordinates from the particles file for the Topaz job.
Thank you,
David