[phenixbb] covalently linked ligand

[Nigel Moriarty]

Charles

If you have a recent version, you can use the command-line program

phenix.ligand_linking
Usage:
  phenix.ligand_linking pdb_file_name


Options:
  --version        show program's version number and exit
  -h, --help       show this help message and exit
  --show-defaults  Display defaults

to get the files needed for phenix.refine. Don't make a "super
residue" as I believe that will make life difficult when you try to
deposit to the PDB.

Cheers

Nigel

PS. Happy to help you directly if you have issues.


On Fri, Jun 8, 2012 at 9:40 AM, Charles Stewart Jr., PhD
<cstewart at salk.edu> wrote:
> Hello all,
>
> I saw a couple of posts on this from a year ago but didn't find a
> conclusive answer to how to tell phenix to insert a covalent bond between
> a cysteine residue  and a bound inhibitor. I have the inhibitor (a small
> molecule) modeled in but haven't figured out how to insert the covalent
> bond. I used PRODRG to generate the inhibitor pdb and eLBOW to generate a
> cif file. The distance between the sulfur on the cysteine and the first
> carbon atom in the inhibitor is 1.8A.
>
> Do I need to run eLBOW using the protein-inhibitor pdb to generate an
> appropriate cif file?
>
> I see in phenix.refine under the PDB interpretation tab their is a box for
> "add link to CIF"....is this where I need to tell phenix to insert the
> covalent bond?
>
> I guess I could just draw the inhibitor-cysteine complex as a modified
> amino acid and try inserting it that way.....
>
> charles
> --
> Charles Stewart Jr., PhD
> Research Associate
> Chemical Biology and Proteomics Laboratory-Noel
> Salk Institute for Biological Studies
> 10010 North Torrey Pines Road
> La Jolla, CA 92037
>
> Phone: (858) 453-4100 x1946
> Fax: (858) 597-0855
> Email: cstewart at salk.edu
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb



-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov