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Bug #7282

closed

appion CTFFIND error

Added by Venkata Dandey over 5 years ago. Updated over 5 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
-
Target version:
-
Start date:
04/18/2019
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.4
Show in known bugs:
No
Workaround:

Description

I am getting this error past two weeks when I try to do CTF estimation through appion. Please see the attached screenshot


Files

Screenshot-1.png (149 KB) Screenshot-1.png Venkata Dandey, 04/18/2019 02:40 PM
Actions #1

Updated by Anchi Cheng over 5 years ago

  • Status changed from New to Assigned
  • Assignee set to Venkata Dandey

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.

Actions #2

Updated by Anchi Cheng over 5 years ago

  • Assignee changed from Venkata Dandey to Shaker Krit

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.

Actions #3

Updated by Sargis Dallakyan over 5 years ago

I have been asking users to do `rm -rf ~/.matplotlib` in #4583, #3749 and elsewhere. I've decided to do this in the code instead. I'm running the same job now as vdandey and it seems to be working.

Actions #4

Updated by Anchi Cheng over 5 years ago

  • Status changed from Assigned to Closed
  • Assignee changed from Shaker Krit to Anchi Cheng

Thanks, Sargis.

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