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Bug #2658
closedconverting IMAGIC to mrc image using imagic_to_mrc() produces header issue for Relion
Status:
Won't Fix or Won't Do
Priority:
Low
Assignee:
-
Category:
Python scripting
Target version:
Start date:
02/12/2014
Due date:
% Done:
0%
Estimated time:
Affected Version:
Appion/Leginon 3.0.0
Show in known bugs:
No
Workaround:
Description
I'm trying to get Relion working inside Appion. Relion produces an error that it does not support VAX floating point conversion. It reaches this conclusion because ( amin > amax ) in the header of the stack file it is reading.
In Appion, the function doing the conversion is:
def imagic_to_mrc(imagic_name, mrc_name, yflip=False):
Relion runs fine doing the conversion outside of Appion with the following batch file:
#!/bin/csh -f setenv IMAGIC_BATCH 1 ### ### change these parameters ### 1) ../relion_recon49/start -- this needs to point to an IMAGIC stack (without the .hed extension) ### 2) ali -- this needs to point to the output .mrcs stack, without the extension ### /opt/Imagic/stand/em2em.e <<EOF IMAGIC MRC 2D MULTIPLE ../relion_recon49/start ali mrcs YES EOF
Anchi, does any of this ring a bell? Have an idea of what is going wrong?
If not, go ahead and assign it back to me and I'll try to track it down. I'm just not familiar with the tools for working with MRCs so I'll have a steep learning curve, and hope to get relion working quickly.
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