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3dem / model-angelo

Automatic atomic model building program for cryo-EM maps
MIT License
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Some questions about format of Input #23

Open zhihao-2022 opened 1 year ago

zhihao-2022 commented 1 year ago

I find that the most format EM maps is .map, but this software needs .mrc. Is the software supports .maps format?

jamaliki commented 1 year ago

Hi,

Yes I believe that should work. Could you try and let me know?

Best, Kiarash

biochem-fan commented 1 year ago

Although most CryoEM programs write only cubic maps with isotropic pixel sizes, the MRC (and CCP4 MAP) formats allow non-cubic boxes and different pixel sizes along each axis. Moreover, the CCP4 MAP format allow non-orthogonal axes https://www.ccp4.ac.uk/html/maplib.html#description.

It would be nice to clarify what is the expectation and check that in the code. Isotropic pixel sizes and orthogonal axes seem reasonable requirements, while supporting non-cubic maps can be useful for elongated proteins.

zhihao-2022 commented 1 year ago

hi, thanks for your effort. 1669039418989 I still find I can't finish the final step, because of the datasets. What datasets are you recommending?

jamaliki commented 1 year ago

Hi!

The database name should be ./scope70_1.75

Could you try this command instead?

hhblits -i output/hmm_profiles/A.hhm -d ./scope70_1.75 -o A.hhr -oa3m A.a3m -M first

Best, Kiarash

zhihao-2022 commented 1 year ago

1669047979724

It is still not working at that moment.

jamaliki commented 1 year ago

It should be ./scop70_1.75 not ./scop_1.75

zhihao-2022 commented 1 year ago

Sorry, it is a typo. But I find that still doesn't work.

1669048540764

zhihao-2022 commented 1 year ago

I guess whether its the datasets' reason

jamaliki commented 1 year ago

Oh sorry, I see the problem. It is the directory structure. So, you need to put in ./scop70_1.75/scop70_1.75