I have attached the map and omit map(after deleting helix) images.
2Fo-Fc(1 sigma)
Fo-Fc(3sigma)
On 5/13/13, Eleanor Dodson <[log in to unmask]> wrote:
> Hard to say without seeing the maps and experimenting. My first check would
> be to set the NTD occupancies to 0.0 - refine the CTD alone, then look at
> the maps in COOT.
>
> Or maybe let an automatic modelling building program such as Buccaneer try
> to rebuild the NTD section, with starting phases from the CTD.
>
> Eleanor
>
>
>
>
> On 13 May 2013 09:04, atul kumar <[log in to unmask]> wrote:
>
>> Dear all,
>>
>> I have solved the structure of my protein by molecular replacement at
>> 2.9A, with Rfactor and Rfree 18 and 22 respectively. Overall everything
>> seems fine, its a two domain protein NTD and CTD, the NTD have high
>> average
>> B factor compared to CTD. A helix of NTD seems to be disordered, I tried
>> different geometric weights but the refined structure does not seem to
>> follow proper geometry for this helix. The B-factor of this helix is very
>> high compared to overall B factor for NTD and omit map shows only some
>> partial density in this region( off course not conclusive). All the
>> homologous structure have helix in this region although with high
>> B-factor.
>> Should I submit the current pdb or need more refinement?
>>
>> thanks and regards
>>
>> Atul Kumar
>>
>
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