Re: [PyMOL] please help-how to generate dimer file from monomer file in pymol

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

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 <jl...@uw...> 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
>
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>
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>
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120