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
