Hi,
You could try to lower the threshold used to contour the maps for these
side-chains (middle mouse "button" if you have a 3 button mouse with a
wheel in the middle). Quite often such side chains have lowish electron
density that does not appear at (say) 1.0 or 1.5 sigma (in the 2mFo-DFc
maps), but that appears at (say) 0.7 sigma. If you delete such
side-chain atoms you'll probably end up with negative difference density
appearing in the difference Fourier after the next round of refinement.
So these residues must be checked individually, much work I know...
"To delete or not to delete, that is the question".
Fred.
Uma Ratu wrote:
> Hello,
>
> I run my model in Coot to do "Temp Fact Variance Analysis".
> There are red bars from the B-factor Variance graphy.
> I click each red bar to exam the residues in Coot. Many of these
> residues do not have the electronic density on their side chains,
> especially Lys residues.
>
> Here is my questions:
>
> 1. The lack of electronic density is the cause of these red-bars?
> 2. How do I fix them? delete the side chains?
>
> The diffraction data is 2A, and data completness is 98.8%.
>
> Thank you for comments
>
> Ros
>
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