This looks to me like a good attempt for GraphEnt. Give it a shot and you might be positively surprised.
Jürgen
Sent from my iPad
On May 13, 2013, at 21:26, "Dale Tronrud" <[log in to unmask]> wrote:
> Sometimes a floppy bit of a protein is even more floppy in a
> particular crystal form. Your maps do not appear to support your
> model of a helix in this location. I would not build it unless
> maps based on later refinement show something reasonable in the
> omit map. (Of course if you leave out the helix, all your maps
> will be omit maps.)
>
> It is quite common to submit models to the PDB that do not
> contain all of the amino acids expected based on the sequence.
> If you can't see where the chain goes you certainly can't be
> expected to build it.
>
> Dale Tronrud
>
> On 05/13/2013 04:23 AM, atul kumar wrote:
>> 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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