I think if you cant see it dont build it, but deposit the data..
There are many (most?) structures with missing loops
Eleanor
Pavel Afonine wrote:
> This might help:
>
> Acta Cryst. (1997). D53, 540-543 Local Improvement of
> Electron-Density Maps
>
> Pavel.
>
> PS> It will be implemented in PHENIX sometime in future, but for the
> moment you will need to so some scripting.
>
>
> On 12/8/2008 11:08 AM, Andy Millston wrote:
>> I am trying to build a model of a 60000 Da protein from the
>> diffraction data collected at 2.0 A resolution. There is a 10-residue
>> stretch that has such bad electron density that even at 0.4 sigma
>> level one can hardly see any well defined density for residues with
>> long side chains.
>>
>> My question is: are such poorly defined regions left unmodeled in
>> protein structures? Or is it conventional to model the whole chain no
>> matter how poor the density? The region in question is in the middle
>> of the chain and has several long side chain residues - both charged
>> and uncharged.
>>
>> AM
>>
>>
>>
>
|