Re: [PyMOL] Changing ligand conformation

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

Hi Mark,

It sounds like you have a couple options. First, you could use PyMOL's
builder (http://www.pymolwiki.org/index.php/Builder; the page needs
updating) to do the trans->cis conversion yourself, by hand. Second,
if you already have the cis structure coordinates, you could issue the
"update" command with the cis coordinates on the trans conformer. Type
"help update" to get help on the update command. The PyMOLWiki has
some more information here: http://www.pymolwiki.org/index.php/Update.

Cheers,

-- Jason

On Fri, Dec 9, 2011 at 4:26 PM, Mark Bostock <mj...@ca...> wrote:
> I have a pdb file of a protein which contains a lysine residue bound to
> a ligand. The ligand has two conformations due to a cis/trans
> isomerisation. I have created a pdb file (also .mol and .mol2) of lysine
> attached to the cis form and would like to replace the
> lysine-ligand(trans) form which is currently in the protein structure
> with the lysine-ligand(cis) form. Does anyone know how to do this;
> mutagenesis only gives me the option of standard amino acids and also
> does not remove the existing ligand.
>
> Many thanks,
>
> Mark.
>
>
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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