Martinizing large proteins/protein complexes

[TommyBiomodelling]

hello there vermouth-martinize people!

I am currently having trouble martinizing a fairly large protein complex (~1MDa). The problem is simply due to the number limit of pdb files (99999 atoms), is there any way to fix this or circumvent this problem when coarse graining with martinize?

I think it could be useful if martinize2 should be able to handle .cif file format, which are more common for structures of large cryo-EM protein complexes in the PDB.

cheers,
Tommy

[csbrasnett]

Hi Tommy,

What command are you using? Are you processing your input file to a clean pdb using grep beforehand? I don't know if that will definitely solve the problem, but it might help.

Thanks for the suggestion of parsing .cif files. We can definitely add it to the list of ongoing enhancements

Chris

[pckroon]

I've had a (very) brief look at a cif reader/writer a couple of years ago already, but never had the time to really sink my teeth into it.
A cif reader/writer would also relax the dssp version requirements quite a bit actually.

[pckroon]

Let me drop this here: https://pypi.org/project/PyCifRW/