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
http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Building+and+Validation#Adding_ligands_to_a_protein.
For cadmium, I think you can enter "CD" for the monomer name (all caps).
The documentation for Refmac has a complete list of recognized monomers
and their 2-3 letter names.
To refine the metal in Refmac with restrained ligand distances, see
http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Refinement#Restraining_metal_ligand_distances_during_refinement_in_REFMAC.
Refmac will create a .cif file with the proper restraints when you try
to run it the first time (and fails). Include the library (.cif) file
when you re-run the job and all will be well.
BTW, if this is a Cd(II) ion, you should really edit columns 76-80 (I
think that's right--you'll see the elements listed in the last 4 columns
of each line of the pdb file) of the PDB file to read "CD+2" and not
"CD ", although in practice this may not make that much difference. But
is is more accurate in terms of X-ray scattering if you indicate the
ionic charge.
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
On 11/28/2011 3:16 PM, Lu Yu wrote:
Hi ALL,
This is the first structure I am working with.
As the title said, I was stuck in the middle of model building using
coot, and I found a big positive peak for Cadmium ion. The coot
program doesn't *know* the cadmium ion when I add a Cd atom there
(under the "place atom at pointer" menu--> "Other" ), and the
refinement program doesn't *know* how to refine this (failed when I
refine the whole structure, and it may need appropriate values as
restraints, but I don't know how to add these values ).
So I am wondering any one can give me any suggestion about, how to add
cadmium ion in the position and do the refinement.
Thanks in advance,
Lu
