[Chimera-users] crystal structure reconstruction

Elaine Meng meng at cgl.ucsf.edu
Mon Oct 1 15:39:48 PDT 2012

Hi Lili,
I can't predict what an MD simulation might show for your protein -- while higher B-factors suggest higher flexibility, you would need to exercise your own scientific judgment on that, or actually perform the experiment (MD).  Chimera doesn't do MD calculations, so you'd have to use some other program.
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 30, 2012, at 5:07 PM, rainy908 at yahoo.com wrote:

> Hi Elaine,
> Thank you for the detailed suggestions.   Following your directions, I re-ran secondary structure calculations in Chimera, and the structure of the loop region did not change.   Unfortunately, there is no experimental density map corresponding to the PDB.
> I performed B-factor analysis on the entire protein, and interestingly, the loop region has the highest B-factor values (yellow) of out all the other regions, including other loops on the protein.  I'd like to clarify that this alpha-helical region corresponds to only 2 amino acids (the entire loop is 9 residues).  
> Given the high B-factor of the loop, if I were to run an MD simulation on this protein to witness conformational changes (~10 ns), I would suspect that the atomic positions of the loop would change anyway?  In other words, the ordered behavior of the 2 residues is transient?
> Thanks again!
> Lili

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