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:del...@delsci.info > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Carlo Zambonelli > Sent: Thursday, May 01, 2008 3:33 PM > To: pymol-users@lists.sourceforge.net > 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 > > -------------------------------------------------------------- > ----------- > This SF.net email is sponsored by the 2008 JavaOne(SM) > Conference Don't miss this year's exciting event. There's > still time to save $100. > Use priority code J8TL2D2. > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java > .sun.com/javaone > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
