[Chimera-users] adding metal ions

Elaine Meng meng at cgl.ucsf.edu
Thu May 1 16:13:42 PDT 2008

Hi Carlo,
Yes, but I don't think it would be very easy - you would have to do  
most of the work!

Option 1 (recommended):
Try to find another structure with similar coordination environment  
that does contain the metal, match the coordinating residues onto the  
corresponding residues in the structure without the metal, and write  
the metal-containing structure as a PDB file "relative to" the other  
Then I would simply text-edit the metal out of the new PDB and into  
the other PDB that was lacking the metal.  This is by far the easiest  
if you can find such a similar structure that already has the metal ion.

Option 2A (depends how precise the position must be):
Build Structure (under Tools... Structure Editing) allows you to  
"Add" an atom.
You would have to put that atom in a "new model" so you could move it  
separately from the structure.  Then you would move it around  
yourself until you think it is in the right place.  Different models  
can be frozen/unfrozen in place using the checkboxes below the  
Command Line or the "Active" checkboxes in the Model Panel.  Then you  
would again write out the "ion" as a PDB file "relative to" the ion- 
lacking structure and then text-edit to add it to that file. I  
wouldn't bother changing the element in the Modify section of Build  
Structure since you can just text-edit the name to the element you  
want when you are doing all that other text-editing.

Option 2B (not recommended):
After you do everything in option 2A, you could read your new PDB  
file back in and attempt to energy-minimize, allowing ONLY the ion to  
move, to get it in a better position.  I am skeptical about this  
option because you have to do a bunch of other stuff before you can  
minimize (fix up the structure by adding missing atoms including  
hydrogens, possibly delete extra hydrogens from histidines  
coordinating the ion, etc.), and currently Fe ions cannot be handled,  
so only Zn++ has any chance of working.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 1, 2008, at 3:37 PM, Carlo Zambonelli wrote:

> I have a pdb file with the coordinates of an apo-enzyme. I know Fe3 
> + 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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