[cctbxbb] crystal packing/unit cell question

Jessica Grant jgrant at smith.edu
Thu Nov 3 12:42:45 PDT 2011

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__" :

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'



>>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 
>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 ?
>cctbxbb mailing list
>cctbxbb at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20111103/d81f1abe/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Picture 10.pdf
Type: application/octet-stream
Size: 37295 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20111103/d81f1abe/attachment-0001.obj>

More information about the cctbxbb mailing list