[phenixbb] metal coordination restrain on alternative conformation

[Zhang yu]

Hi Nigel,

Another question. How do I let phenix.refine know that all atoms in my
ligand should have the same occupancy for one conformation? The occupancy
refinement in phenix.refine assigned different occupancies to atoms in one
conformation.

Thanks

Yu






On Tue, Oct 1, 2013 at 6:10 PM, Zhang yu <phenixzyfish at gmail.com> wrote:

> Thanks
>
>
> On Tue, Oct 1, 2013 at 1:54 PM, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:
>
>> I ran
>>
>> phenix.metal_coordination
>>
>> and got the attached. Pass it to phenix.refine.
>>
>>
>> On Mon, Sep 30, 2013 at 6:53 PM, Zhang yu <phenixzyfish at gmail.com> wrote:
>>
>>> Hi Nigel,
>>>
>>> Thanks. Please see attached PDB file. The structure has two molecules in
>>> one ASU. Each of molecule contains 6 protein chains and three Nucleic-acid
>>> chains (i.e. chain A, B, C, D, E, F, G, H and I for molecule 1; chain K, L,
>>> M, N, O, P, Q, R, and S for molecule 2)
>>>
>>> There is only one nucleoside-triphosphate and its cognate MG++ in each
>>> molecule having alternative conformations (named as conformation A and B).
>>> The desired restrains are as follows,
>>>
>>> In molecule 1,
>>> atom_selection_1 = name MG,B  and chain N and resname MG and resseq 2004
>>> atom_selection_2 = name OD2   and chain N and resname ASP and resseq  739
>>> distance_ideal = 2.090000
>>>
>>> atom_selection_1 = name MG,B  and chain N and resname MG and resseq 2004
>>> atom_selection_2 = name O3G, B and chain S and resname CMP and resseq
>>>  2001
>>> distance_ideal = 2.090000
>>>
>>> atom_selection_1 = name MG,B  and chain N and resname MG and resseq 2004
>>> atom_selection_2 = name O1B,B and chain S and resname CMP and resseq
>>>  2001
>>> distance_ideal = 2.090000
>>>
>>> atom_selection_1 = name MG,A  and chain N and resname MG and resseq 2004
>>> atom_selection_2 = name O1B,A and chain S and resname CMP and resseq
>>>  2001
>>> distance_ideal = 2.090000
>>>
>>> atom_selection_1 = name MG,A  and chain N and resname MG and resseq 2004
>>> atom_selection_2 = name O1G,A and chain S and resname CMP and resseq
>>>  2001
>>> distance_ideal = 2.090000
>>>
>>> In molecule 2,
>>> atom_selection_1 = name MG,B  and chain D and resname MG and resseq 2004
>>> atom_selection_2 = name OD2   and chain D and resname ASP and resseq  739
>>> distance_ideal = 2.090000
>>>
>>> atom_selection_1 = name MG,B  and chain D and resname MG and resseq 2004
>>> atom_selection_2 = name O3G, B and chain I and resname CMP and resseq
>>>  2001
>>> distance_ideal = 2.090000
>>>
>>> atom_selection_1 = name MG,B  and chain D and resname MG and resseq 2004
>>> atom_selection_2 = name O1B,B and chain I and resname CMP and resseq
>>>  2001
>>> distance_ideal = 2.090000
>>>
>>> atom_selection_1 = name MG,A  and chain D and resname MG and resseq 2004
>>> atom_selection_2 = name O1B,A and chain I and resname CMP and resseq
>>>  2001
>>> distance_ideal = 2.090000
>>>
>>> atom_selection_1 = name MG,A  and chain D and resname MG and resseq 2004
>>> atom_selection_2 = name O1G,A and chain I and resname CMP and resseq
>>>  2001
>>> distance_ideal = 2.090000
>>>
>>>
>>>
>>>
>>>
>>> On Mon, Sep 30, 2013 at 6:31 PM, Nigel Moriarty <nwmoriarty at lbl.gov>wrote:
>>>
>>>> Can you send the residues involved?
>>>>
>>>> Nigel
>>>>
>>>> NB. Any files sent to me will be held in strictest confidence.
>>>>
>>>>
>>>>
>>>> On Mon, Sep 30, 2013 at 12:51 PM, Zhang yu <phenixzyfish at gmail.com>wrote:
>>>>
>>>>>  Hi everyone,
>>>>>
>>>>> My structure contains a metal coordinating to some residues, one of
>>>>> which has alternative conformations. Phenix doesn't pickup the residue with
>>>>> alternative conformation when I tried to generate metal restrains using
>>>>> ready.set.
>>>>>
>>>>> Any idea? Thanks
>>>>>
>>>>> Yu
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>>
>>>>
>>>
>>
>>
>> --
>> 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
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20131003/9418ac07/attachment-0001.htm>