Problems to run refine2D for input mrcs generated from EMAN hed(img) file #413
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davidh99720
changed the title
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Is your pixel size correct? If not, specify in |
Yes, it is correct. I figure it out after thinking it over. I change the star file to the following and it works. Thank you!data_ loop_ |
I am trying to do a simulation to test the power of RELION2.1 refine2D algorithm.
The input is a EMAN hed(img) file and I convert it to mrcs file using e2proc2d.py
Then, I import it as mrcs file and write bash to generate a particles.star file for it. The head of it is attached in the appendix in the end.
However, when I try refine2D, I encounter the following error:
ERROR:
image.cpp::calculateBackgroundAvgStddev(): No pixels in background are found. Radius of circular mask is too large.
File: /home/xxx/Software/relions/relion/src/image.cpp line: 246
Any idea of how to fix it will greatly appreciated!
Appendix:
data_
loop_
_rlnCoordinateX #1
_rlnCoordinateY #2
_rlnClassNumber #3
_rlnAnglePsi #4
_rlnAutopickFigureOfMerit #5
_rlnImageName #6
_rlnMicrographName #7
_rlnMagnification #8
_rlnDetectorPixelSize #9
0 0 -999 -999 -999 000001@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000002@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000003@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000004@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000005@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000006@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000007@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000008@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000009@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000010@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000011@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000012@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000013@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000014@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000015@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000016@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000017@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000018@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000019@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000020@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000021@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000022@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000023@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000024@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000025@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000026@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000027@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000028@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
0 0 -999 -999 -999 000029@Import/job001/GroEL-proj-shft10-addnoise150.mrcs null 100000 1
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