parameter file error

Submitted by chaoqi on Thu, 2017-07-27 17:59

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Frealign

Hi everyone,

I am a frealign new user. I use Region did 2d classification and use Select in relion2 selected the good particles. Then I use the script on the website converted the star file to par file. But after I run frealign, it still shows the error about parameter file.

Starting refinement...
ERROR: Something wrong with parameter file.
If input file contained film#, defocus 1, defocus 2, astig. angle,
please make sure that numbers are separated by spaces, not commas.

Does anyone have suggestions about it? Thank you very much!!!

Best regards,
Chao

chaoqi Tue, 2017-08-01 11:26

Hi Niko,

I prepared the parameter file like this:

1 24990.2 25486.4 2.41
1 24990.2 25486.4 2.41
1 24990.2 25486.4 2.41
1 24990.2 25486.4 2.41
1 24990.2 25486.4 2.41
1 24990.2 25486.4 2.41
1 24990.2 25486.4 2.41

I use the constant number for the particle number.No commas,just spaces.
But there is still an error message:
Starting refinement...
ERROR: Something wrong with parameter file.
If input file contained film#, defocus 1, defocus 2, astig. angle,
please make sure that numbers are separated by spaces, not commas.
Cycle 2: refining particles 1 to 385, class 1 Tue Aug 1 17:19:51 CEST 2017
Cycle 2: refining particles 386 to 770, class 1 Tue Aug 1 17:19:51 CEST 2017
Cycle 2: refining particles 771 to 1155, class 1 Tue Aug 1 17:19:51 CEST 2017
Cycle 2: refining particles 1156 to 1540, class 1 Tue Aug 1 17:19:51 CEST 2017

Is the defocusangle in Relion the same parameter with astigmatic angle here? If there are different, I didn't find the astigmatic angle in my star file. Do you think the error come from this parameter?

Thank you very much.

Best regards,
Chao

niko Tue, 2017-08-01 17:19

The parameter file you prepared should have been replaced withe a reformatted parameter file that has more columns. Could you most the first line of the reformatted parameter file here so I can see what it looks like?

chaoqi Tue, 2017-08-01 17:41

Hi Niko,

These are the first several lines after the script transform.

1 -103.45 18.29 135.17 -12.03 -4.63 10000 1 24990.2 25486.4 2.41 100.00 -500 1.0000 20.00 0.00
2 -63.73 93.82 -1.92 -4.63 1.72 10000 1 24990.2 25486.4 2.41 100.00 -500 1.0000 20.00 0.00
3 -63.17 115.43 -147.93 2.78 8.07 10000 1 24990.2 25486.4 2.41 100.00 -500 1.0000 20.00 0.00
4 -27.27 109.55 93.37 8.07 -3.57 10000 1 24990.2 25486.4 2.41 100.00 -500 1.0000 20.00 0.00
5 161.17 108.51 3.68 -7.80 14.42 10000 1 24990.2 25486.4 2.41 100.00 -500 1.0000 20.00 0.00
6 -124.29 120.84 149.68 -0.39 1.72 10000 1 24990.2 25486.4 2.41 100.00 -500 1.0000 20.00 0.00

I did 3d classification with class=1 using relion. Someone said that it is better do one round of 3d classification or refinement before move to frealign. I don't know it is true or not.

Best regards,
Chao

chaoqi Wed, 2017-08-02 03:42

Dear Niko,

The new parameter file is produced directly with the script on the website (relion to frealign). It is not working. Then I modified the file, just take out the particle number and defucus values. But unfortunately, it is still not working.

Best regards,
Chao