Or refine the occupancies with Refmac...
Roberto
From my iPhone
On 27 Jul 2012, at 11:04, "Tim Gruene" <[log in to unmask]> wrote:
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> Dear Ngo Duc Tri,
>
> I would manually set the occupancy of chain A to about 30% and chain
> B's to 70% and try again.There is density for chain A present in the
> second picture, it is just weaker.
>
> Cheers,
> Tim
>
>
> On 07/27/12 10:01, Tri Ngo wrote:
>> Dear ccp4bb,
>>
>>
>> I am working on refinement of an enzyme structure. I notice an
>> alternative conformation (gauche+ and gauche-) on both residues Phe
>> and Tyr.
>>
>>
>> Here is the image of electron density before refinement. Based on
>> the different map intensity, I am quite sure there is an
>> alternative conformation on both positions.
>>
>>
>> http://i50.tinypic.com/29zaoap.jpg
>>
>>
>> However, after running occupancy refinement by Phenix, I don't see
>> the density map at the gauche- conformation of Tyr residue. Please
>> take a look at the image 2.
>>
>>
>> http://i50.tinypic.com/anzfrn.png
>>
>>
>> So do you think the gauche- conformation of Tyr exists in this
>> structure. Should I keep it in the final model because there is no
>> positive map there?
>>
>>
>>
>> Thank you very much for your input.
>>
>>
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
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