[cctbxbb] crystal packing/unit cell question -p.s.

Pavel Afonine pafonine at lbl.gov
Thu Nov 3 16:18:19 PDT 2011


Yes, in the end, I think it's a good idea to add a command like

iotbx.pdb.expand_to_p1
(available in phenix. too)

with a few popular options and the default behavior that would suit most 
popular one.

Pavel

On 11/3/11 4:02 PM, Nat Echols wrote:
> Neither of these will work, for the reasons that were already stated -
> with sites_mod_positive=False, the symmetry mates do not necessarily
> end up with most atoms in the minimal unit cell with origin at 0,0,0,
> and with sites_mod_positive=True, all atoms are in the unit cell, but
> the protein chains are chopped up.  Neither of these shows how the
> crystal is packed.  Doing so requires sampling translations of the
> fractional coordinates.
>
> On Thu, Nov 3, 2011 at 2:29 PM, Pavel Afonine<pafonine at lbl.gov>  wrote:
>> Hi Jessica,
>>
>> try with sites_mod_positive=False (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.
>>
>> Pavel
>>
>>
>> On 11/3/11 12:42 PM, Jessica Grant wrote:
>>
>> 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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