Jenna,
Use PyMOL to download the biological unit:
fetch 1b8e, type=pdb1
split the states out (you'll notice it's a two-state object)
split_states 1b8e
You can also create symmetry expansion via, A > Generate > Symmetry Mates >
within X A, from your original object.
Cheers,
-- Jason
On Tue, Apr 6, 2010 at 12:36 AM, JiangJiang Liu <jli...@uwo.ca> wrote:
> **
> Hello all,
>
> When I open the pdb file 1B8E (a homodimer protein) through
> pymol I can only see a monomer shown in the screen. Now I know the
> biological dimer is produced through crystallographic symmetry operations in
> pymol. To generate the dimer, I think I need to convert these remark comands
> (list below) to be a readable commands by the pymol program. Does anyone
> know how to do this conversion? Or what's the commands for crystal symmetry
> operation?
> Thank you very much!
>
> Sincerely
> Jenna Liu
> PS:
> REMARK 350 BIOMOLECULE:
> 1
> REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT:
> DIMERIC
> REMARK 350 APPLY THE FOLLOWING TO CHAINS:
> A
> REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000
> 0.00000
> REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000
> 0.00000
> REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000
> 0.00000
> REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000
> 0.00000
> REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000
> 0.00000
> REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000
> 33.43000
>
> <http://www.mail-archive.com/pymol-users@lists.sourceforge.net/>
>
> <http://www.mail-archive.com/pymol-users@lists.sourceforge.net/>
>
>
> ------------------------------------------------------------------------------
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> proactively, and fine-tune applications for parallel performance.
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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