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 ******************************************************* On Thu, Mar 1, 2012 at 9:26 AM, Uma Ratu <rosiso2...@gmail.com> 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 > >
