extract particles

[yokomaz]

Hi all! I'm working with pytom_tm to perform template matching on my tomograms, and I've got particles list file xx_particles.star.

I would like to extract particles' subtomograms from the tomograms.

I checked pytomGUI and its requires a .xml file as job file to extract particles.

I‘d like to ask if there are any utils to convert result from pytom_tm to pytom? or should I use other softwares to extract particles subtomograms.

[sroet]

Hey @yokomaz, doesn't the convert.py utility from PyTOM work for you? (that should be able to take in a star file and output an xml)

[yokomaz]

Hey @sroet ! thank you for your response, I tried with convert.py to convert my particle star file to xml, it needs to remove some columns in pytom_tm generated star file.

['rlnSearchStd', 'rlnLCCmax', 'rlnCutOff']

but when I used .xml file converted by convert.py, excuted particle picking, error arised Exception: This XML is not an JobDescription.

I have following results in my pytom_tm folder are
_angles.mrc,

_extraction_graph.svg,

_job.json

_particles.star

_scores.mrc

I tried to convert _job.json, and it showed that The given input file format is not supported: json

I'd like to ask which file should be converted to xml file as job file

[sroet]

Please try converting it to a particle list file (ending on .pl) instead of going to an xml. (particle lists are a special kind of xml file for PyTOM)
Also, I will transfer this issue to the PyTOM repo, as I feel this is more a PyTOM issue and not necessarily a pytom-match-pick issue