ctffind output
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Hello,
When I run ctffind4 on tomography tilt series consisting of 61 frames. I get output containing ctf parameters ( if I correctly understand) as average values for the tilt series. Please see below:
# Output from CTFFind version 4.1.14, run on 2022-06-27 21:18:54
# Input file: ./tomo_wt_002.mrc ; Number of micrographs: 1
# Pixel size: 3.356 Angstroms ; acceleration voltage: 300.0 keV ; spherical aberration: 2.70 mm ; amplitude contrast: 0.07
# Box size: 512 pixels ; min. res.: 40.0 Angstroms ; max. res.: 10.0 Angstroms ; min. def.: 40000.0 um; max. def. 60000.0 um
# Columns: #1 - micrograph number; #2 - defocus 1 [Angstroms]; #3 - defocus 2; #4 - azimuth of astigmatism; #5 - additional phase sh
ift [radians]; #6 - cross correlation; #7 - spacing (in Angstroms) up to which CTF rings were fit successfully
1.000000 60066.507812 58577.039062 -16.516852 0.000000 0.081746 9.875126
Instead, I wish to get an output containing ctf parameters for each 61 images within the tilt series. Like below
# Output from CTFFind version 4.1.14, run on 2022-06-27 21:18:54
# Input file: ./tomo_wt_002.mrc ; Number of micrographs: 1
# Pixel size: 3.356 Angstroms ; acceleration voltage: 300.0 keV ; spherical aberration: 2.70 mm ; amplitude contrast: 0.07
# Box size: 512 pixels ; min. res.: 40.0 Angstroms ; max. res.: 10.0 Angstroms ; min. def.: 40000.0 um; max. def. 60000.0 um
# Columns: #1 - micrograph number; #2 - defocus 1 [Angstroms]; #3 - defocus 2; #4 - azimuth of astigmatism; #5 - additional phase sh
ift [radians]; #6 - cross correlation; #7 - spacing (in Angstroms) up to which CTF rings were fit successfully
1.000000 60066.507812 58577.039062 -16.516852 0.000000 0.081746 9.875126
2.000000 61066.507812 59577.039062 -17.516852 0.000000 0.081746 9.875126
3.000000 61266.507812 57577.039062 -18.516852 0.000000 0.081746 9.875126
.....
61.00000 ......
Is there a flag that I am missing as an input for cttfind4?
Thanks,
Elena
Hi Elena, what are the…
Hi Elena,
what are the parameters you are using?
My guess is you answered
Input is a movie (stack of frames):
with Yes, which will cause ctffind to assume the images are frames of a movie and calculate an average ctf value.
Best,
Johannes
Hello Johannes, Thanks that…
In reply to Hi Elena, what are the… by jojoelfe
Hello Johannes,
Thanks that solved the issue.
Elena