Thanks Eleanor, John and Nigel for your tips. Actually it seems to be a problem
of geometry restraints.
Nigel, let me edit the .def file as John recommended and then I'll contact you.
Best regards
Gerardo Andrés Libreros
Laboratório de Biologia Estrutural Aplicada
Universidade de São Paulo
São Paulo- Brasil.
Enviado desde mi iPhone
> El 7 dic 2017, a las 17:08, Nigel Moriarty <nwmoria...@lbl.gov> escribió:
>
> Gerado
>
> John is correct that you can modify the restraints model to include a
> covalent bond. Also in more recent version of Phenix, if the input geometry
> is approximately correct, the bond can be automatically linked.
>
> If you send me the input file, I'll take a closer look.
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709 Email : nwmoria...@lbl.gov
> Fax : 510-486-5909 Web : CCI.LBL.gov
>
>> On Thu, Dec 7, 2017 at 9:51 AM, Tanner, John J. <tanne...@missouri.edu>
>> wrote:
>> You can add a covalent bond by modifying this part of the PHENIX .def file
>> via the gui:
>>
>> geometry_restraints.edits {
>> excessive_bond_distance_limit = 10
>> bond {
>> action = *add delete change
>> atom_selection_1 = None
>> atom_selection_2 = None
>> symmetry_operation = None
>> distance_ideal = None
>> sigma = None
>> slack = None
>> }
>>
>> John J. Tanner
>> Professor of Biochemistry and Chemistry
>> Chair, Biochemistry Department Graduate Admissions Committee
>> Department of Biochemistry
>> University of Missouri-Columbia
>> 117 Schweitzer Hall
>> 503 S College Avenue
>> Columbia, MO 65211
>> Phone: 573-884-1280
>> Fax: 573-882-5635
>> Email: tanne...@missouri.edu
>> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
>> Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
>> Office: Schlundt Annex 203A
>>
>>> On Dec 7, 2017, at 11:40 AM, Eleanor Dodson
>>> <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>>>
>>> Is that format correct?
>>> Eleanor
>>>
>>>> On 7 December 2017 at 17:32, gerardo andres
>>>> <0000130afa955101-dmarc-requ...@jiscmail.ac.uk> wrote:
>>>> Hi everyone. I´m trying to make a covalent bond between a cystein residue
>>>> of a protein and its ligand, but always that I do the refinement by
>>>> Phenix, the ligand is placed outside of its electronic density. I edited
>>>> the PDB file like this:
>>>> LINK SG CYS A 215 C02 LIG C 1 , but this is not
>>>> working. Someone has some idea to address this problem?
>>>>
>>>> Thanks,
>>>>
>>>> Gerardo
>>>
>>
>
