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ccpem / roodmus

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Starfile writing via gemmi/ccpem-pipeliner #4

Open JatGreer opened 7 months ago

JatGreer commented 7 months ago

Issue 17 from gitlab Add some analysis/utils.py code to write out starfiles with relion-compatible format(s). Identify the useful formats and whether .stars need to be written from scratch, or copied+updated only. Then add the required functionality

JatGreer commented 7 months ago

We need to review whether we need this functionality to complete work required for publishing Roodmus paper(s)

JatGreer commented 7 months ago

This package has functionality to convert csparc to .star file. Intermediate is a data frame. We could use it to output the .yaml config files as .star https://github.com/asarnow/pyem/tree/master/pyem

MJoosten commented 4 months ago

The current write_starfile utility exists and can be used to turn a df_truth style data frame into a set of starfiles that resemble the output of a particle picking job in RELION. This starfile can then be loaded and used to extract particles. However, no orientation information can be available in this version of the starfile. I would like to update the utility to allow for the creation of starfiles that can be used directly to specify particle orientations

MJoosten commented 2 months ago

Update on progress: I've added the ability to write a data-style starfile which can contain information about the orientations of each particle. This starfile can then be loaded in Relion and the particles can be re-extracted and processed further. However, in testing I tried to produce a simple reconstruction by using the backprojection function in Relion and was not able to get a density map out that resembled the protein. My guess is that there is still some convention difference in the way Relion notes orientations that I may have to resolve