Re: [ccp4bb] covalent bond

[Andres Libreros]

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  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.  
>> 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 
>>> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>>> 
>>> Is that format correct?
>>> Eleanor
>>> 
 On 7 December 2017 at 17:32, gerardo andres 
 <130afa955101-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
>>> 
>> 
> 

Re: [ccp4bb] Conserved water

[Andres Libreros]

Thanks everyone for the tips. Actually, I need this information to improve my 
analysis on drug/protein interaction.
Best regards:)

Gerardo A. Libreros
Universidade de São Paulo
Laboratório de Biologia Estrutural Aplicada

Sent from my iPhone

> On 7 Jun 2017, at 18:34, Jared Sampson  wrote:
> 
> Hi Gerardo - 
> 
> Something based on distance alone (and not e.g. H-bonding network) could be 
> done in a straightforward fashion in PyMOL:
> 
> select close_wats, (object1 and solvent) within 1 of (object2 and solvent)
> hide everything, solvent
> as nb_spheres, close_wats
> 
> This would give you only the waters in object 1, but you could expand this 
> logic and include the object2 waters as well.
> 
> select close_wats, close_wats or ((object2 and solvent) within 1 of 
> (object1 and solvent))
> 
> Hope that helps.
> 
> Cheers,
> Jared
> 
> 
>> On Jun 6, 2017, at 7:30 PM, gerardo andres 
>> <130afa955101-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Hi everyone, does anyone know any strategy or program (besides pywater) to 
>> identify conserved waters in a protein?
>> 
>> Thanks, 
>> 
>> Gerardo
>