[phenixbb] covalently linked ligand

[ChenTiantian]

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 <pafonine at lbl.gov> 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
>> <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
>>>
>>
>>
>>
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-- 
Tiantian
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