Hi,

I want the tutorial to complete Relion21 tutorial to assess if I installed it correctly.

At step 3 “CTF estimation”, I get this warning message "WARNING: skipping, since cannot get CTF values for”.
Note that the message is not truncated : it stops after “for”.

As one could expect this output and from the runtime, which is 0 second, output files are empty.

This is the command ran by relion:

relion_run_ctffind_mpi --i MotionCorr/job002/corrected_micrographs.star --o CtfFind/job005/ --CS 2 --HT 300 --AmpCnst 0.1 --XMAG 10000 --DStep 3.54 --Box 512 --ResMin 30 --ResMax 7.1 --dFMin 5000 --dFMax 50000 --FStep 500 --dAst 100 --use_noDW --ctffind_exe /usr/local/relion/bin/ctffind --ctfWin -1 —is_ctffind4

This is the content of _ctffind4.com:

#!/usr/bin/env csh
/usr/local/relion/bin/ctffind > CtfFind/jobfoo/_ctffind4.log << EOF
CtfFind/jobfoo/
CtfFind/jobfoo/.ctf
3.54
300
2
0.1
512
30
7.1
5000
50000
500
no
no
yes
100
no
no
EOF
exit 0

What I understand from this file is that relion doesn’t give the correct mrc input file to ctffind (c.f. line 3).

I’m running ctffind v4.1.8 from Jun 15 2017.

Has anyone encountered this problem?

I guess there is an obvious misconfiguration problem from my side, but can’t find it.

Any help would be greatly appreciated.
Best regards.
--
Benoist Laurent, PhD
Research Engineer CNRS
Institut de Biologie Physico-Chimique - FRC 550
13, rue Pierre et Marie Curie - F-75005 Paris
Tel. +33 [0]1 58 41 52 08
--
Benoist
Room S05 (basement)
52 08