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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 ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1