Don't forget you will need to adjust the contour level to see something with occupancy 0.3 - easily done with coot
eleanor
On 27 Jul 2012, at 11:25, Steiner, Roberto wrote:
> 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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