Some questions about format of Input

[zhihao-2022]

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

[jamaliki]

Hi,

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

Best, Kiarash

[biochem-fan]

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]

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

[jamaliki]

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]

It is still not working at that moment.

[jamaliki]

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

[zhihao-2022]

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

[zhihao-2022]

I guess whether its the datasets' reason

[jamaliki]

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