gctf

[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: [email protected]
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

TIME<<<<<< PREPARATION: 0.505697s
Reading file: movie_aligned.mrc
TIME<<<<<< READING: 0.051089s
.
TIME<<<<<< FFT: 1.039372s

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

[sthennin]

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 Henning,
No I couldn't find such a file. I'll look into it again after the holiday.
Merry Christmas to the Focus team !