Re: [PyMOL] Add a small molecule to a protein

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

Hi Nir,

If you have the structure of the small molecule, why not try the following:

  load yourProtein.pdb
  load yourSmallMol.pdb
  create complex, *

The new object called "complex" will now have the protein and small molecule.

If you don't--and want something for illustration only--then you can
convert it from SMILES to pdb using lots of different software.  After
this, you can throw it into a docking program and use the output for
your image.  Again, I stress "for illustration only."

Cheers,

-- Jason

On Thu, May 6, 2010 at 11:57 PM, Nir Qvit <nir...@gm...> wrote:
> Hi,
> Is there is a way to add a small molecule to a protein after loading a
> pdb file of the protein from the database?
> We are trying to make a figure of a protein and a small molecule that we
> know that is interacting with the protein. In the database there is the
> structure of the protein only.
> What will be the best way to add the small molecule to the protein for a
> schematic figure?
> thanks for your help,
> Nir
>
> Nir Qvit, Ph.D.
> Postdoctoral Fellow
>
>
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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