If you edit the PDB file "by hand", then you should have no problems. Some folks might cringe at this, but this does work:
1. Like Roger Rowlett said, "place atom at pointer". You can place a chloride there. Be sure to add to your molecule and not a new molecule. 2. Save the coordinates to a PDB file. 3. Edit the newly saved PDB file with the Chloride designation with an editor (emacs is great) and change the Chloride to a Cadmium. What does a Cadmium look like in a PDB file? I don't have a clue, but I would search for "cadmium" at rcsb.org and save a PDB file with a cadmium in it. Then you can see what a cadmium looks like in the example PDB file and mimic that in your file. Jim ________________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Roger Rowlett [rrowl...@colgate.edu] Sent: Monday, November 28, 2011 3:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] how to add Cadmium ion to structure and do the refinement Lu, To add a metal ion to a structure, you can use "place atom at pointer" or "Get Monomer...". I usually use the latter. For instructions see ....
