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Refine Template not recording alignment metadata for some micrographs

tlaughlin

Refine Template not recording alignment metadata for some micrographs

Hello,

I am encountering an issue of Refine Template after running Match Template not recording the alignment data into the database.

The output.mrc files reflect that refinement was performed (see attached).

I am using the distributed binary of cistem2-alpha, running refine_template on 1000 micrographs, and running 48-64 processes for these refinement jobs.

Any insight on what to do in order to get the match metadata written to the database/accessible?

Thanks for the help!

Wed, 05/22/2024 - 21:51

jojoelfe

Hi,

 

unfortunately the Refine Template page in the GUI is not working. There are two options, you can either use the refine_template cli program or you can just do a manual refinement job using the template as a reference. (What you do depends a lot on what you are trying to get out of it.)

 

Johannes

Thu, 05/23/2024 - 01:46

tlaughlin

Good to know.

I am trying to both refine initial hits in a template matching run against both the original template and an alternate template with an additional subunit then evaluate the SNR ratios. 

When running refine_template from the command line, is there a straight-forward way to extract the alignment metadata and SNR scores from the .mrc outputs?

Thu, 05/23/2024 - 15:07

jojoelfe

There is a program called make_template_result that takes the mrc outputs, finds the peaks, and spits out the results both on the commandline and to a xyz_coordinates file (that should also include angles and scores).

 

Clearly still a few rough edges, sorry.