Dear all,

To quote a message sent last week: "I am probably being an idiot, but…“. :-)

But: I am running auto-picking in Relion 3. My data (aligned, summed *.mrc files) are saved in a "central" storage folder, and I can’t/don’t want to move them from there (because this is where our data is supposed to be stored) or copy them (because that's a waste of space). So I soft-link to the /storage/*.mrc files from inside a folder called micrographs in my working directory (i.e. micrographs/myfile.mrc -> /storage/myfile.mrc). When running auto-picking, the program picks properly, writes the output properly, BUT internally, it gets confused as to where it wrote the output and thinks up weird paths that exist nowhere in any star file. These paths reflect the soft link to the storage location. 

For example, when trying to assess the picks in the viewer, the program tries to read the auto-pick star files from:

AutoPick/job039/../../XX/Micrographs/Titan2_0002_ali_DW.mrcmicrographs/Titan2_0002_ali_DW_autopick.star 

However, there is obviously no such location, and therefore the viewer fails to read the star file when I attempt to inspect the picks (using the display tool in the auto-picking job).

The path should be (and these *autopick.star files DO exist):

AutoPick/job039/micrographs/Titan2_0002_ali_DW_autopick.star

The appended (inserted) path, between "job039" and "micrographs"

../../XX/Micrographs/Titan2_0002_ali_DW.mrc 

is where the soft link points (i.e. "ls -l" inside micrographs gives: Titan2_0002_ali_DW.mrc -> ../../XX/Micrographs/Titan2_0002_ali_DW.mrc). Somehow the program concatenates these paths. The inserted path changes when I change the location to which my soft links point.

Notably, extraction based on the output written by this auto-pick job does work. So this seems to be an isolated issue with the auto-picking/display (plus manual picking and import) tools and soft linking.

Is this a bug? Otherwise, any clues what I should do differently?

Thanks, and sorry for that convoluted description,

Basil

########################################################################

To unsubscribe from the CCPEM list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1