Hi Chad,
Good question. The PDB header to 1rmv tells us we can generate the
biological unit using "REMARK 350" from the PDB. Recently a script
was added to the PyMOLWiki that creates just such structures. This
script was then improved by those in the PyMOL community. Please see
http://www.pymolwiki.org/index.php/BiologicalUnit for the code.
Here's what I typed to get it to work after saving the script to disk
as "BiologicalUnit.py"
# run the script, this let's PyMOL know about
# the script and it's functions
run ~/biologicalUnit.py
# get the PDB
fetch 1rmv, async=0
# read the symmetry field from the PDB
symMat = readSymmetry("/path/to/my/1rmv.pdb", "1rmv")
# apply the transformations from the header
biologicalUnit("mates", "1rmv", symMat)
The PDB file 1rmv made 49 transformed copies. I ray traced the image
and put on the wiki page for the script as another example.
Cheers,
-- Jason
On Mon, Oct 18, 2010 at 6:43 PM, Chad Simmons <[email protected]> wrote:
> Hello,
>
> Does anyone know how to display PDB files that are determined by fiber
> diffraction? The default just shows a single peptide, when in fact it is
> supposed be a bunch of peptides interacting with one another to make a fiber.
>
> Thanks a lot.
>
> Chad
> ***************************
> Chad R. Simmons
> Researcher
> Biodesign Institute
> at Arizona State University
> P.O. Box 875601
> Tempe, AZ 85287
> Office: (480) 727-6495
> Lab: (480) 727-0428
> Fax: (480) 727-0396
>
>
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Jason Vertrees, PhD
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