[phenixbb] covalently linked ligand
Nigel Moriarty
nwmoriarty at lbl.gov
Fri Jun 8 12:50:09 PDT 2012
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
>
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--
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
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