Output for Relion 1.3

Submitted by Ruda Santos on Fri, 2015-08-28 06:41

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Magdistortion

Hello,

I'm trying to use the corrected CTF magnification with Relion 1.3 but there is no .log output which I can extract the values. Is there a way to generate these files from the final corrected CTF? Thanks!

Best,

Ruda

Ruda Santos Fri, 2015-08-28 09:27

Hi Niko,

I'm trying to make the ctf star file for Relion. I wrote a script to batch process the mag correction but when I try to use the --only_make_star option in Relion i get this error:

ERROR: cannot find line with Cs[mm], HT[kV], etc values in Feb07_00.58.35_sum_ctffind3.log
File: src/ctffind_runner.cpp line: 297

When I ran the mag estimate and mag correction there was no output as in ctffind4 such as *_avrot.txt, *.com and *.log. I'm assuming that Relion needs the .log files since it's the input that ctffind_runner.cpp is asking for. I tried with ctffind3 and ctffind4 as well. The commands I used are:

CTFFIND 4.0.16

`which relion_run_ctffind` --i "test_list.star" --o "micrographs_ctf.star" --ctfWin -1 --CS 2.7 --HT 300 --AmpCnst 0.1 --XMAG 49505 --DStep 5 --Box 512 --ResMin 100 --ResMax 7 --dFMin 5000 --dFMax 50000 --FStep 500 --dAst 0 --ctffind3_exe ../../../Software/ctffind4.0.16/ctffind "--old_school_input --only_make_star" &

CTFFIND3

`which relion_run_ctffind` --i "test_list.star" --o "micrographs_ctf.star" --ctfWin -1 --CS 2.7 --HT 300 --AmpCnst 0.1 --XMAG 49505 --DStep 5 --Box 512 --ResMin 100 --ResMax 7 --dFMin 5000 --dFMax 50000 --FStep 500 --dAst 0 --ctffind3_exe ../../../Software/ctf/ctffind3.exe --only_make_star &

Thanks!