[phenixbb] covalently linked ligand

Nigel Moriarty nwmoriarty at lbl.gov
Fri Jun 8 12:50:09 PDT 2012


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

  phenix.ligand_linking pdb_file_name

  --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.



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

More information about the phenixbb mailing list