How to output as mmcif

[git-jrwang]

I notice there a mmcif output in check-in feature. There is no description in document. I look into source code and I can't figure out how to do it from command line. Can anbody tell me? Thanks a lot.

[krab1k]

Hi, sorry for the late response. The mmcif file with the calculated charges is created automatically when the computation ends. The file should be available in the directory specified by the --chg-out-dir option. Does that work for you?

[git-jrwang]

Thanks for the replying. I do find that a .fw2.cif file generated. However, I have another problem.

I was told that I should add hydrogen to PDB file for correctly calculate partial charge. I use either Pymol or ChimeraX to generate a new .pdb or .mif file with hydorgen position after I download file from PDB. Then I use Chargefw2 to calculate partial charge. Using 3ggw as an example, the .pdb as input to .pqr as otput works fine. .cif format as input to .pqr format as output is also fine. But .cif as input to .cif output does not work. The output file is empty, It gives something like "category of atom is missing". I cannot figure out why. If I use the mmcif file directly download from PDB, it works fine.

1. Do I really need to add hydrogen into file before I use your program to calculate partial charge?
2. I can work with .pqr file format. But the .pqr file generated will change seq_id. For example, 3ggw has 27, 27A, 27B, ... .pqr format will change all to 27. Is there any way to maintain the original seq_id?
3. Do you have any idea to fix the .mmcif input with hydrogen problem?