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Hi Jessica,<br>
<br>
try with <b>sites_mod_positive=False</b> (this is what I mentioned
this morning in my previous email). I think (but not sure) one of
them should do "what you want" . I just tried. Run the attached
script with the PDB file of your choice, and compare the results.<br>
<br>
Pavel<br>
<br>
<br>
On 11/3/11 12:42 PM, Jessica Grant wrote:
<blockquote cite="mid:a0624080ccad89b1d504e@%5B10.0.1.3%5D"
type="cite">
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<title>Re: [cctbxbb] crystal packing/unit cell
question</title>
<div>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.</div>
<div><br>
</div>
<div>code looks like this:</div>
<div><br>
</div>
<div><b>from iotbx.file_reader import any_file</b></div>
<div><b>import sys</b></div>
<div><b>from mmtbx import utils<br>
<br>
def run (args) :<br>
<x-tab> </x-tab>pdb_file = args[0]</b></div>
<div><b><x-tab>
</x-tab>pdb_inp = any_file(pdb_file,
force_type="pdb").file_object</b></div>
<div><b><x-tab> </x-tab><br>
<x-tab> </x-tab>xray =
pdb_inp.xray_structure_simple()<br>
<x-tab> </x-tab>uc =
xray.expand_to_p1(sites_mod_positive=True)<br>
<br>
<x-tab> </x-tab>outfile = open("unit_cell.pdb",
"w")<br>
<br>
</b></div>
<div><b><x-tab>
</x-tab>utils.write_pdb_file(xray_structure = uc,
pdb_hierarchy =
pdb_inp.construct_hierarchy(), out = outfile)</b></div>
<div><b><br>
</b></div>
<div><b>if __name__ == "__main__" :</b></div>
<div><b><x-tab>
</x-tab>run(sys.argv[1:])</b></div>
<div><br>
</div>
<div><br>
</div>
<div>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'</div>
<div> </div>
<div>Maybe?</div>
<div><br>
</div>
<div>Jessica</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<blockquote type="cite" cite="">
<blockquote type="cite" cite="">1) isn't this a method of the
X-ray
structure object, not one of the PDB objects?</blockquote>
</blockquote>
<blockquote type="cite" cite=""><br>
expand_to_p1 is a method from xray/structure.py. I just used it
yesterday.<br>
<blockquote type="cite" cite="">2) won't it split up molecules
to keep
the sites all inside the unit cell?<br>
<br>
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.)</blockquote>
</blockquote>
<blockquote type="cite" cite=""><br>
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.<br>
Anyway, it's faster to try than typing this email: try both,
save
xray_structure as PDB file and open it in PyMol.<br>
<br>
What is 'symexp' function in PyMOL ?<br>
<br>
Pavel<br>
<br>
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