Has someone helped you with this?
Re coot and PT - I thought you could just add an atom and call it PT?
Here is the pdb format for a metal compared to a OE1
ATOM 312 OE1 GLN B 99 -28.427 -30.882 26.585 1.00 20.00
B O
HETATM 1594 PT PT H 1 0.000 0.000 7.669 0.33 34.88
PT
ie atom name PT moved one place to left
"residue name" PT
Atom type PT one place to left relative to O
Re the links
If you run refmac with "review restraints" it will suggest links to the
PT. You should check them for sensible chemistry, then include them in
refinement.
Eleanor
On 09/27/2011 02:07 PM, Jose Arcadio wrote:
Dear coot users:
I in order to solve my protein structure via experimental phasing, I
soaked my crystals in potassium tetracyanoplatinate (II) hydrate. In my
(almost) final model I could identify two binding sites where two
metionines are coordinating (I guess) a platinum ion. The two heavy atom
sites had high occupancy (I did the phasing using sharp). I still can
not find a way to improve the geometry, bond length and coordinates of
the sites. Moreover, when I calculate the clashing score using REDUCE
and PROBE, the programs indicate a horrible cluster of clashes in the
vicinity of the platinum sites. I placed the platinum using the tool:
add atom at pointer in coot (the platinum ion option was not present in
the selection window, therefore I typed "PT". Coot always tells me in
the terminal the following message:
Debug:: there were 2 types with no dictionary
PT
PT
I also was checking how were defined the LINK records in PDB files with
platinum bound; however, I did not manage to place it properly in my
model (in order to refine them). Obviously I am doing something wrong.
Here are the questions:
Do you know a proper way [for dummies :-) ] of placing a platinum or
heavy metal atom in a final model?
Do you know how do the platinum sites have to be defined in the PDB file?
Do you know which is the best way to generate a .cif file or dictionary
in order to refine the platinum sites?
Thanks in advance for your time, wish you a nice day!
All the best
Jose Arcadio Farias Rico
PhD Student
Höcker Group (Protein Design)
http://www.eb.tuebingen.mpg.de/research-groups/birte-hocker/protein-design
MPI for Developmental Biology, Spemannstr. 35, 72076 Tübingen, Germany
Tel: +49 7071 601 365
Fax: +49 7071 601 305
E-Mail: [email protected]
