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3dem / model-angelo

Automatic atomic model building program for cryo-EM maps
MIT License
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Can not handle map with nxstart/nystart/nzstart!=0 #77

Open wang3702 opened 1 year ago

wang3702 commented 1 year ago

I tested model-angelo on map EMD-6149 and EMD-3133. The final modeled structure will be shifted because current pipeline did not handle the nxstart well. You can consider to use this function https://github.com/kiharalab/CryoREAD/blob/main/data_processing/Unify_Map.py before passing the map into further processing

jamaliki commented 1 year ago

Hi,

Ah, is this in case the global origin does not point to the correct origin and needs to be shifted by the n[xyz]start?

wang3702 commented 1 year ago

Yes. I mean n[xyz]start is part of the coordinate system, you should include script to process it. Actually, for some older maps, these fields are more commonly used.

jamaliki commented 1 year ago

Interesting, I thought we already handled this in our load_mrc function. So this is an issue with EMD-6149? I will take a look.