Thanks everyone, for the input.  I have written a little script using your help.  Attached is an image -- the green is the output of my script, the blue is the original pdb file.

code looks like this:

from iotbx.file_reader import any_file

import sys

from mmtbx import utils

def run (args) :
pdb_file = args[0]

        pdb_inp = any_file(pdb_file, force_type="pdb").file_object

       
        xray = pdb_inp.xray_structure_simple()
  uc = xray.expand_to_p1(sites_mod_positive=True)

outfile = open("unit_cell.pdb", "w")

 

        utils.write_pdb_file(xray_structure = uc, pdb_hierarchy = pdb_inp.construct_hierarchy(), out = outfile)

if __name__ == "__main__" :

        run(sys.argv[1:])

It doesn't look like it is doing quite what I want.  Oh...I just had the thought that perhaps I should apply the symmetry operators before using 'expand_to_P1'

 

Maybe?

Jessica

1) isn't this a method of the X-ray structure object, not one of the PDB objects?

expand_to_p1 is a method from xray/structure.py. I just used it yesterday.

2) won't it split up molecules to keep the sites all inside the unit cell?

I'm getting annoyed that it's not easier to do this kind of lattice generation for proteins, so I may just try coding it myself later today or tomorrow.  (I'd like to figure out something analogous to the 'symexp' function in PyMOL, but I think that's a little more work.)

I can't imagine what can be easier than this? If you don't want to "split" copies to be all atoms from 1 to -1, then I guess sites_mod_positive=True (or False, I don't remember) should probably simply multiply copies.
Anyway, it's faster to try than typing this email: try both, save xray_structure as PDB file and open it in PyMol.

What is 'symexp' function in PyMOL ?

Pavel

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