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scipion-em / scipion-em-sphire

Plugin to use Sphire programs within the Scipion framework
GNU General Public License v3.0
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Write out box files with original filename? #8

Closed andreanans closed 5 years ago

andreanans commented 5 years ago

Hi,

I noticed that cryolo outputs .box files as coordinates but they have been renamed to mic1, mic 2 etc. It would be super helpful if the box files retained the original name in case users want to move into Relion standalone etc.

delarosatrevin commented 5 years ago

Hi, yes, we decided to go for shorter names here. I would prefer to keep like that (to avoid really long filenames with path included). Maybe I should consider an open issue of a general ' relion - export coordinates protocol' where the user could decide to choose the output file names. What do you think?

andreanans commented 5 years ago

Yes it would be super helpful to have a general relion export coordinates function to write out star files with the full micrograph name.

One workaround we are using at the moment is to run a relion extract with a small box size (2x2). We take the *coords.star file to use in relion standalone. However we have to do some renaming and remove the 'coords' part of the filename.

delarosatrevin commented 5 years ago

Ok, thanks again for the feedback. I think I will close this issue and raise the priority of the relion - export coordinates that has already been proposed here: https://github.com/scipion-em/scipion-em-relion/issues/76