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Subject:

Re: e2motion.py problems

From:

"James S." <[log in to unmask]>

Reply-To:

James S.

Date:

Wed, 6 Jun 2018 13:09:30 +0000

Content-Type:

text/plain

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text/plain (1 lines)

Additionally I've tried using a single class-average image from Relion as the Reference image for the alignment (I selected one good class-average in relion and imported the class_averages.mrcs file into eman using the 'import particle' tool which created a job16-class_averages.hdf file which I tried to use with the e2a2d_align.py I got a whole screen of script the last of which said /home/loca/software/eman/2.2/lib/python2.7/lib-dynload/_json.soAborted 
 
Again a m2d_01 directory was created containing the there files but still an error message that no particle alignment data found for iter= 1 
 
Ta  
 
-----Original Message----- 
From: Collaborative Computational Project in Electron cryo-Microscopy [mailto:[log in to unmask]] On Behalf Of James S. 
Sent: 06 June 2018 13:39 
To: [log in to unmask] 
Subject: [ccpem] e2motion.py problems 
 
I've used e2motion.py in the past to get an animation of the movement range of my protein however the last couple of times trying it I cant seem to get it to work; 
 
when using; 
e2motion.py --path m2d_01 --iter 1 --threads=16 
 
I get the message: 
 
Warning: no particle alignment data found for iter= 1 
 
I had previously used the: 
 
e2a2d_align.py particles/particleMRC.hdf particles/RefImageMRC.hdf --align rotate_translate_tree --aligncmp ccc --cmp ccc --threads=16 
 
I thought this had worked as it created the directory 'm2d_01' which contained three files: 
 
0_a2d_parms.json 
particle_parms_01.json 
refimg_01.hdf 
 
Any idea where this might be going wrong? 
 
The particle.hdf was an mrc stack containing 1663 particle images. The Reference Image was also an mrc stack from a single Relion Class Average containing 191 images. Should the Reference image be just a single class-average image and if so do you know how I would get this from relion? 
 
Thanks for your help, 
 
Sonya 
 
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