Appion

Have you ever run ctffind4 through appion at 3 Å pixel successful before ? The error occus while it is making the evaluation plots. I wonder if it is ever done at such large pixel size before.

Please test with these python commands on node-48 with appion environment.

You can find '19apr18d_07gr_03sq_02hl_02en-pow_avrot.txt' in Venkat's rundir shown in his screenshot.

from appionlib.apCtf import ctffind4AvgRotPlot
avgrotfile = '19apr18d_07gr_03sq_02hl_02en-pow_avrot.txt'
outputpng = ctffind4AvgRotPlot.createPlot(avgrotfile)

This may be specific to the node he ran from. I was able to run it on node-39

The full appion command to test on the single image is

/opt/myamisnap/bin/appion ctffind4.py --ampcontrast=0.07 --fieldsize=1024 --resmin=50 --resmax=4 --defstep=0.1 --numstep=25 --dast=0.05 --min_phase_shift=10 --max_phase_shift=170 --phase_search_step=10 --num_frame_avg=7 --runname=ctffind4run2anchi --rundir=/gpfs/appion/acheng/19apr18d/ctf/ctffind4run2anchi --commit --projectid=63 --session=19apr18d --no-wait --no-continue --bestdb --expid=8911 --jobtype=ctfestimate --mrclist=19apr18d_gr_00007gr_00003sq_v02_00002hl_00002en.mrc

You must change rundir to be a directory that you have permission to write to, though.

Thanks, Sargis.