[phenixbb] covalently linked ligand

Pavel Afonine pafonine at lbl.gov
Fri Jun 8 15:58:49 PDT 2012

Hi Nigel,

can we do it as part of a default phenix.refine, as well as 
phenix.metal_coordination? I see a growing pressure to do this... I 
think there is more harm not doing this at all then doing this always 
but not very optimally.

Let's keep this in mind and discuss once we have a chance.


On 6/8/12 12:50 PM, Nigel Moriarty wrote:
> 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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