Ros,

I haven't used the  "Temp Fact Variance Analysis" in Coot, but can guess that the red bars indicate increased b-factor compared to the average of your protein model?

If so, then:

1. The lack of electronic density is the cause of these red-bars?

Likely yes. If there is no density to support the position of the side chain, then you will see an increase in B-factor.

2. How do I fix them? delete the side chains?

This question has been under debate in our community recently.

If I recall correctly (and my opinion) is you should leave the side chains as they are and let the b-factor be an indication of the uncertainty of their position. 

I'm willing to bet these side chains are surface residues, or in a mobile part of our protein.

A good thing to compare is the average b-factor of your entire model compared to these residues, as well as the b-factor of these specific side chains compared to  main chain atoms.

Hope this helps clarify.

Sincerely, 

Kelly Daughtry

*******************************************************
Kelly Daughtry, Ph.D.
Post-Doctoral Fellow, Raetz Lab
Biochemistry Department
Duke University
Alex H. Sands, Jr. Building
303 Research Drive
RM 250
Durham, NC 27710
P: 919-684-5178
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On Thu, Mar 1, 2012 at 9:26 AM, Uma Ratu <[log in to unmask]> 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