No micrographs could be matched with segment files

[Сергей Назаров]

Hi Carsten,

spring_v0-83-1449

I have an error that microgrpahs cannot be matched with corresponding segment (or box) files:

Microgrpah XXX is ignored could not be matched with a segment file.

I attached the report.log file and stdout.log file - output from command line. In stdout.log file you can see that the segment does find the .box files.

Thank you in advance.

Best,

Sergey Nazarov

EPFL LBBS

Lausanne

[Carsten Sachse]

Dear Sergey,

1. It looks like your naming of box and mrc files is not corresponding. You have the following names:

/lbbspc19-scratch/snazarov/Phi32/C-CINA_phi32_and_7-11/orig_mrc/2014-05-14_12_35_53_aligned.mrc and

/lbbspc19-scratch/snazarov/Phi32/C-CINA_phi32_and_7-11/orig_mrc/2014-05-14_12_35_53_aligned_cpsd_hlx.box

The box files need to have the same name as the micrograph just a change in file ending:

/lbbspc19-scratch/snazarov/Phi32/C-CINA_phi32_and_7-11/orig_mrc/2014-05-14_12_35_53_aligned.box

2. Your output stack needs to have a proper file name

xyz.hdf

Best wishes,

Carsten

[Сергей Назаров]

Well, it looks like I found the possible cause of error - the file name might be too long. The segment procedure goes further, however it can't find the information in spring.db file, since I shortened the name of input files, and I have to re-run ctf estimation.

Upcoming question, is there any way not to run ctf estimation again with spring but to use previous estimations instead? Because I already did this with ctffind directly, than I did ctf estimation with relion, and now with spring - result is the same, however hundreds of files are duplicated/

Thank you in advance.

Best,

Sergey Nazarov

[Сергей Назаров]

Dear Carsten

Thank you, I just recently found the same solution, the .mrc file and the .box file has to be the same.

It is a little bit confusing from the Segment manual, in the example the Micrograph name is cs_scan034.tif, 

and the Segment coordinates is scan034_boxes.txt. But in description it says: Input: file with identical name of corresponding micrograph.

Anyway, thank you for the assistance!

Best,

Sergey

On Wednesday, 17 June 2015 19:23:45 UTC+2, Сергей Назаров wrote: