Hi Matthieu,
Thank you. Yes, this is a known bug. It will be fixed in the next beta
version (ie soon).
Sjors
> Hi,
>
> I'm having a problem working with relion 2.0 beta when the micrographs are
> given as symbolic links in the 'Micrographs' folder of the project. The
> tutorial mention the possibility to use symbolic links. I work on
> GNU/linux.
>
> The 'Import' and "Manual picking' steps both work. However, in the manual
> picking job folder the program creates as many folders as picked
> micrographs which are of formed by the concatenation of these 4 strings:
> - the path to the original micrograph (i.e. the target of the symbolic
> link), truncated to 99 characters.
> - 'Micrographs/'
> - the micrograph name without the '.mrc' extension
> - '_manualpick.star'
>
> Thus there is no 'ManualPick/job<N>/Micrographs/' folder (When manually
> picking without symbolic links in the 'Micrographs' folder, the program
> just create a 'Micrographs' folder inside the job folder and all the
> *_manualpick.star files are stored there).
>
> My problem arise when I run 'Particule extraction': it complains it does
> not find the paths
> 'ManualPick/job<N>/Micrographs/<micrographName>_manualpick.star'
>
> And indeed they do not exist. Putting the *_manualpick.star files in a
> 'ManualPick/job<N>/Micrographs' directory is a workaround for the
> particule extraction but then these files are no longer properly
> associated to the manual picking job.
>
> In the 'Micrographs' directory of the project, replacing the symbolic
> links by the data they point to solve the problem but I'd like to avoid to
> duplicate my datasets to process them.
>
> Thanks for any suggestions,
>
> Matthieu
>
>
>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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