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 structure. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb 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. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/ editing.html 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. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/ minimize.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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