[phenixbb] covalently linked ligand

[Nigel Moriarty]

Tiantian

You can use a number of automatic linking options but the blanket option is
link_all=True.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, 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

On Mon, Sep 21, 2015 at 7:39 PM, ChenTiantian <chentiantian2010 at gmail.com>
wrote:

> 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
>>>>
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>>>>
>>>
>>>
>>>
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>
>
>
> --
> Tiantian
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