[phenixbb] Creating dictionary restraints for a LINK

Nigel Moriarty nwmoriarty at lbl.gov
Mon Apr 2 09:27:52 PDT 2012


I'm afraid you'll have to venture out the GUI and use the command-line
version for this particular program. You'll need to source the
appropriate setup file for your shell and run the command. If you have
trouble setting up the command-line environment, contact me off-line.

Cheers

Nigel

On Mon, Apr 2, 2012 at 9:09 AM, Mario Sanches <mariosan at gmail.com> wrote:
> Hi Nigel,
>
> "phenix.ligand_linking"  is not an option with my current installation
> (PHENIX version dev-1021). I have "phenix.ligand_identification"  and "
> phenix.ligandfit" .
>
> Mari Sanches
>
>
> On Mon, Apr 2, 2012 at 11:57 AM, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:
>>
>> Mario
>>
>> You can use
>>
>> phenix.ligand_linking model.pdb
>>
>> to generate the links between ligands and residues. Don't forget to
>> look in the .geo to ensure the links are made once you add the files
>> to the phenix.refine input.
>>
>> Nigel
>>
>> On Mon, Apr 2, 2012 at 8:29 AM, Mario Sanches <mariosan at gmail.com> wrote:
>> > I have a question regarding link dictionary generation. Nigel helped me
>> > with
>> > a molecule dictionary last week (thank you Nigel) so the molecule is
>> > refining well now. This molecule is covalently bound to on of the
>> > residues.
>> > I tried generating a dictionary that describes both the molecule and the
>> > link but so far phenix.refine is ignoring it. Again, the molecule itself
>> > refines very well but the link is not there. What is the best way to
>> > define
>> > it?
>> >
>> > Thank you very much.
>> >
>> >
>> > --
>> > Mario Sanches
>> > Postdoctoral Researcher
>> > Samuel Lunenfeld Research Institute
>> > Mount Sinai Hospital
>> > 600 University Ave
>> > Toronto - Ontario
>> > Canada
>> > M5G 1X5
>> > http://ca.linkedin.com/in/mariosanches
>> >
>> > _______________________________________________
>> > phenixbb mailing list
>> > phenixbb at phenix-online.org
>> > http://phenix-online.org/mailman/listinfo/phenixbb
>> >
>>
>>
>>
>> --
>> 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
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
>
>
> --
> Mario Sanches
> Postdoctoral Researcher
> Samuel Lunenfeld Research Institute
> Mount Sinai Hospital
> 600 University Ave
> Toronto - Ontario
> Canada
> M5G 1X5
> http://ca.linkedin.com/in/mariosanches
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>



-- 
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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