Re: [PyMOL] appending metal ions

[DeLano S. <de...@de...>]

Carlo,

PyMOL isn't really a builder, but can do something like the following:

First 

load my_enz.pdb

Then, move the camera around so that the place where you want the Zn is in
the center of the screen (e.g. that point in space doesn't move when you
rotate the camera).  Now enter the following command to add a zinc atom:

pseudoatom my_enz, elem=Zn, name=Zn, resn=Zn, resi=1

You can then manually position the atom, by switching the mouse mode to
3-button-editing:

edit_mode

and then ctrl-right-click-and-draging the atom around

To create another Zinc with a different residue number:

pseudoatom my_enz, elem=Zn, name=Zn, resn=Zn, resi=2

And so forth.  When you're done, write out the new pdb file.

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Carlo Zambonelli
> Sent: Thursday, May 01, 2008 3:33 PM
> To: pym...@li...
> Subject: [PyMOL] appending metal ions
> 
> I have a pdb file with the coordinates of an apo-enzyme. From 
> biochemical data I knowFe3+ and Zn2+ are essential for 
> catalysis; I also know some of the residues involved in 
> coordination of Fe3+ and Zn2+. Can I position 2 ions in the 
> structure so that they are correctly oriented relative to the 
> coordinating residues? My ultimate goal is to create a PDF 
> file containing also the metal ions.
> Thanks,
> Carlo
> 
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