reextracting refine3D data star particles from fresh MotionCorr not working anymore #524
Comments
Yes.
Did you do this before import? Another way is to convert STAR files by |
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The Import job should have written a warning: If didn't, please let me know. |
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I did it after import, but I modified the star file in the Import/job004 folder, not the original one I selected for import. I assume this can't make a difference? My workaround was to extract coordinates for each referenced micrograph and import those coordinates. This works well. Not sure which info I'm losing though? Tilt / Rot information seems to be lost on re-extraction anyhow. Are rlnGroupNumber/Name preserved after reextract normally? Regarding box sizes - the approach seems to be kind of mixed now. Both pixel size and box size are encoded in .mrc files, but you are reading pixel size from the star file, and the box size from the mrcs file. Do you think it would make sense rather to consolidate it and include rlnImageBoxSize as a metadata parameter rather than reading mrcs files? Best J |
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This was reported on import, yes |
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Tried importing the "fixed" star file. There was no error in import this time. I'm still getting the error on attempt to reextract. There is a possibility it's due to soft links in the path I guess? I have encountered this in the past. |
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When you imported the fixed STAR file, does the output has the The box size is determined when a file is converted from 3.0 to 3.1 during Import. Thus, the image files must be available when importing.
Did you use the full path in the link? |
Earlier versions of RELION (and some external programs) didn't write the pixel size to the MRCS header. Thus we don't trust the field. |
Ok, I see I made a mistake now. I tried to reimport the file that I fixed in the Import folder, and that one didn't work because it already had the optics table without the image dimensions. When I fixed the original and imported it fixed, it did work in the end.
using relative paths in links, because we have diferent mount points in different systems, and absolute paths would only work in one (/absolute/path/no1/parent1/parent2/target vs /i/am/mounted/differently/parent1/parent2/target). Relative paths work very well in this case, even Windows resolves them correctly. Most programs we use are (or seem) agnostic to whether the file is a symlink or not, and agnostic to how the symlink is defined. If the shell can see and resolve it properly, so do the programs. Not sure why is this not the case with relion, but I assume you do some kind of optimized file access which makes it behave this way. I also tried first continuing the last iteration of the refinement in the old project. It gave me the correct star file incl box size (I see now it's a part of an optics group). This one imports and reextracts correctly in the new folder as well. Thanks for your answers! |
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To note, in the end the symlinks were not an issue (even though it's nested symlinks some of which have relative paths). |
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(I edited your markup)
Yes. This makes sense.
The problem is that RELION tries to expand symbolic links for job aliases into real paths (e.g. Refine3D/class1 => Refine3D/job123). We do our best to keep symbolic links to somewhere outside the project directory (../somewhere/Refine3D/class1) but there are many corner cases this fails. Relative links sometimes work, but absolute links are always safer (because we never expand anything starting from |
Trying to re-extract particles from a data.star file from Refine3D in relion 3.0.6 in 3.1.
I made a new project and re-did motionCorr and CtfFind from scratch.
I copied the data.star to the new project folder and adjusted the rlnMicrographName to the path of the fresh MotionCorr and CtfFind.
Got a "ObservationModel::getBoxSize: box sizes not available" error.
Thought it might be because in the new version it is trying to read the box size from the mrcs files. Adjusted the rlnImagePath in the imported star file so that it points to the locations of the mrcs files in the old project folder. Confirmed "Display" works for these particles from relion 3.1 gui. Still got the same error.
head of Import/job004/from_190919_struct_A_job070_data.star:
head of CtfFind/job003/micrographs_ctf_beamtilt.star:
Environment:
Dataset:
Job options:
note.txtin the job directory):Error message:
Please cite the full error message as the example below.
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