[cctbxbb] crystal packing/unit cell question

[Jessica Grant]

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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