Peter,
Coot can insert a metal ion for you just fine. Just choose "Place Atom
At Pointer" from the Model/Fit/Refine menu and type "ZN" (case
sensitive) in the "Other" Box. OF course, you should put the pointer
where you want to add the atom first. Alternatively, you can do the same
with "File...Get Monomer" by typing in "ZN". What Coot won't do (yet)
for you is a nice, real-space restrained refinement of ligands and metal
for you, but Refmac can do this if you adjust your ligands to reasonable
metal-ligand bond distances. Instructions (might be kludgy, but works)
can be found at
http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Refinement#Restraining_metal_ligand_distances_during_refinement_in_REFMAC.
I have to update these pages to be consistent with the latest version of
the CCP4 suite, but the directions should be close enough for government
work for now.
I would further recommend manually editing the atom name in columns
77-80 of your PDB file to read "ZN+2" instead of "ZN ". This should
allow Refmac to use more accurate scattering factors for the metal ion,
although in practice it probably doesn't make that big a difference in
your protein model.
Cheers,
_______________________________________
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: [email protected]
On 5/4/2012 2:27 PM, Peter Hsu wrote:
Hi all,
Forgive the rather ignorant question, but I'm rather new to using coot/model
building and I'm trying to model in a Zn2+ atom but coot doesn't seem to have
the files for a Zn atom in its database. I'm not sure where to start
looking/how to write a file that defines a Zn2+ atom and to have it properly
coordinated by the Cys residues. Can anyone give me any pointers?
Thanks in advance for the help,
Peter
