sthennin
commented
6 years ago Hi Benoit, this could be that you have a different gCTF version than we, and that the version you have produced different output files. You are using Version: /usr/local/bin/gctf v1.18, updated on 2017-05-10 I have to check, which version we use.
Do you find a file named movie_aligned_EPA.log somewhere? If not, you could also out-comment that call to the plotter script. It is a python script that tries to make a nice plot as result from gCTF. It is cosmetics, you don't really need it.
aseedb
Hi again, Next problem : gCTF run is giving this error `Processing done successfully. Average defocus = 2.722 microns CTF Figure of Merrit: 0.251149 Estimated resolution limit by EPA: 0.000000
======================================================================================================================================================================================================= ==== Plotting CTF =====================================================================================================================================================================================
############################process_ctf finished.############################# Traceback (most recent call last): File "/home/cryoadmin/focus/scripts/proc/CTF_plotter.py", line 12, in data_file = open(infile) IOError: [Errno 2] No such file or directory: 'movie_aligned_EPA.log'
And the part of the log that gives the options used for gctf is here:======================================================================================================================================================================================================= ::==== Calling gctf ===================================================================================================================================================================================== :=======================================================================================================================================================================================================:: ::Running: :: :: /usr/local/bin/gctf.sh :: --apix 1.05294 :: --kv 300.0 :: --cs 2.7 :: --AC .100 :: --defL 2000.0 :: --defH 50000.0 :: --defS 250.0 :: --astm 1500 :: --bfac 100 :: --resL 80.0 :: --resH 3.2 :: --boxsize 512 :: :: :: :: movie_aligned.mrc ::
Version: /usr/local/bin/gctf v1.18, updated on 2017-05-10 Author: Kai Zhang@MRC Laboratory of Molecular Biology Contact: kzhang@mrc-lmb.cam.ac.uk Description: This is a simplified version of Gctf for CTF determination.
Opening movie_aligned.mrc for initial test and preperation .......
User input parameters: --apix 1.053 --kv 300.00 --cs 2.70 --ac 0.10 --defL 2000.00 --defH 50000.00 --defS 250.00 --astm 1500.00 --bfac 100.00 --resL 80.00 --resH 3.20 --boxsize 512
All parameters to be used: General options: --apix 1.053 --dstep 14.000 --kv 300.00 --cs 2.70 --ac 0.10 Phase shift options: OFF --phase_shift_L 0.00 --phase_shift_H 180.00 --phase_shift_S 0.00 --phase_shift_T 1 --only_search_ps 0 --cosearch_refine_ps 0 Advanced options: --bfac 100.00 --defL 2000.00 --defH 50000.00 --defS 250.00 --astm 1500.00 --resL 80.00 --resH 3.20 --boxsize 512 --overlap 0.50 --convsize 42 --refine_2d_T 1 --smooth_resL 1000.00 --do_validation 0 EPA related options: --do_basic_rotave 0 --do_basic_rotave 0 --do_EPA 0 --refine_after_EPA 0 High resolution refinement options: --do_Hres_ref 0 --Href_resL 15.00 --Href_resH 4.00 --Href_bfac 50.00 --Href_PS_err 2.00 --Href_U_err 100.00 --Href_V_err 100.00 --Href_A_err 5.00 Bfactor estimation options: --estimate_B 1 --B_resL 15.00 --B_resH 6.00 Movie options: --do_mdef_refine 0 --mdef_ave_type 0 --mdef_aveN 7 --mdef_fit 0 Local refinement options: --do_local_refine 0 --local_radius 1024.00 --local_boxsize 512 --local_overlap 0.50 --local_avetype 0 Correction options:
--do_phase_flip 0 Validation options:
--do_validation 0 Input CTF parameters for refinement: --refine_input_ctf 0 --ps_init 0.00 --defU_init 20000.00 --defV_init 20000.00 --defA_init 0.00 --B_init 200.00 --ps_err 10.00 --defU_err 500.00 --defV_err 500.00 --defA_err 15.00 --B_err 50.00 --input_ctfstar NULL Diagnosis CTF output options: --ctfout_resL 100.00 --ctfout_resH 2.21 --ctfout_bfac 50.00 I/O options: --ctfstar micrographs_all_gctf.star --logsuffix _gctf.log --boxsuffix _automatch.star --write_local_ctf 0 --plot_res_ring 1 --skip_check_mrc 0 --skip_check_gpu 0 --gid 0 --do_unfinished 0
All 1 files to be searched and refined: movie_aligned.mrc
Defocus_U Defocus_V Angle CCC 26986.35 27459.01 56.89 0.251149 Final Values
Processing done successfully.`
Not sure what is wrong... Cheers Benoit