Hi,
Please try the latest version (4.1.13).
It has many improvements over earlier versions.
Also look at the log files (not run.out/run.err
but *_ctffind4.log) to see if the program produced some errors.
Running the program directly, not via RELION, is useful
in diagnosing whether the problem is in CTFFIND itself or
RELION's wrapper.
> --phase_min 0 --phase_max 175
It was sometimes helpful to limit the phase shift search range
to say 30 to 120 deg in earlier versions, although I found that
the default works fine in almost all cases with 4.1.13.
> --ResMin 20 --ResMax 3
I often use the default (30 to 5 A).
Best regards,
Takanori Nakane
On 2019/01/27 5:54, Uhnsoo Cho wrote:
> Dear all,
>
> I am calculating CTF estimation using Ctffind (4.1.9) in relion 3.0.
> The dataset is collected from Krios using the volta phase plate.
>
> Here is the command line I used:
>
> `which relion_run_ctffind_mpi` --i
> MotionCorr/job007/corrected_micrographs.star --o CtfFind/job014/ --CS 2.7
> --HT 300 --AmpCnst 0.07 --XMAG 10000 --DStep 1.06 --Box 512 --ResMin 20
> --ResMax 3 --dFMin 3000 --dFMax 7000 --FStep 500 --dAst 100
> --do_phaseshift --phase_min 0 --phase_max 175 --phase_step 10
> --ctffind_exe /opt/bin/ctffind --ctfWin -1 --is_ctffind4
>
> After the run, here is the info from micrographs_ctf.star
>
> # RELION; version 3.0-beta-2
>
> data_
>
> loop_
> _rlnMicrographName #1
> _rlnCtfImage #2
> _rlnDefocusU #3
> _rlnDefocusV #4
> _rlnCtfAstigmatism #5
> _rlnDefocusAngle #6
> _rlnVoltage #7
> _rlnSphericalAberration #8
> _rlnAmplitudeContrast #9
> _rlnMagnification #10
> _rlnDetectorPixelSize #11
> _rlnCtfFigureOfMerit #12
> *_rlnCtfMaxResolution #13*
> _rlnPhaseShift #14
> MotionCorr/job007/Micrographs/FoilHole_13562412_Data_13565940_13565941_20190115_1919-11016.mrc
> CtfFind/job013/Micrographs/Foi
> lHole_13562412_Data_13565940_13565941_20190115_1919-11016.ctf:mrc
> 5000.000000 5000.000000 0.000000 -1.08229e+24 300.0
> 00000 2.700000 0.070000 10000.000000 1.060000 0.000000
> *25.000000 * 87.500112
> MotionCorr/job007/Micrographs/FoilHole_13562481_Data_13565940_13565941_20190115_2053-11075.mrc
> CtfFind/job013/Micrographs/Foi
> lHole_13562481_Data_13565940_13565941_20190115_2053-11075.ctf:mrc
> 5000.000000 5000.000000 0.000000 -1.08229e+24 300.0
> 00000 2.700000 0.070000 10000.000000 1.060000 0.000000
> *25.000000 * 87.500112
> MotionCorr/job007/Micrographs/FoilHole_13557492_Data_13565940_13565941_20190115_0252-10440.mrc
> CtfFind/job013/Micrographs/Foi
> lHole_13557492_Data_13565940_13565941_20190115_0252-10440.ctf:mrc
> 5000.000000 5000.000000 0.000000 -1.08229e+24 300.0
> 00000 2.700000 0.070000 10000.000000 1.060000 0.000000
> *25.000000* 87.500112
>
>
> It seems like Max resolution is 25A, which suggests something was wrong.
> Is there anyone who knows what might be wrong during the process?
> Any suggestion would be appreciated.
>
> Uhnsoo Cho
>
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