Re: [phenixbb] covalently linked ligand

Hi Pavel, What's the latest state of this default function to form an unusual covalent bond? I think it would be great useful. Tiantian On Sat, Jun 9, 2012 at 6:58 AM, Pavel Afonine wrote:

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.

Pavel

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 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: [email protected]

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