Re: [PyMOL] Displaying PDB files that were determined via fiber diffraction

[Jason V. <jas...@sc...>]

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 <Cha...@as...> 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
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
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