Dear All: Thank you very much for your comments.
I did not notice that this issue has been dicussed lately. Thank you for your inputs regards Ros On Thu, Mar 1, 2012 at 9:38 AM, Kelly Daughtry <kddau...@bu.edu> wrote: > 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 >> >> > >
