[Chimera-users] crystal structure reconstruction

Elaine Meng meng at cgl.ucsf.edu
Sun Sep 30 10:47:47 PDT 2012

Hi Lili,
I'm not sure what the person advising you meant -- I don't think it would make any sense to use molmap, since that would just simulate a density map from the coordinates, which are what you are unsure about in the first place.

My only ideas for examining this possibly dubious helical assignment are:

(a) look at B-factor values for the loop, which will give some idea of disorder, for example command:
rangecolor bfactor min blue mid red max yellow
(or see graphical interface "Render by Attribute" under Tools... Structure Analysis. It shows a histogram of the values.)  

However, if the loop is constrained by the crystal structure, it may still have low B-factors, and ** there is nothing in Chimera that will predict for you the intrinsic flexibility of the loop **.  I believe you would need to use some other program that simulates motions or uses some empirical criteria to predict flexibility.

... if your doubts are more toward whether the coordinates are really helical or whether they well represent the original density map, the following may be useful ...

(b) re-run secondary structure assignment calculations in Chimera.  Different methods produce partially different results even for exactly the same atomic coordinates because their criteria differ, so where the authors thought there was a helix, other methods might not. If you open Model Panel (from Favorites menu) there is a "compute SS" button on the right with which you can try recalculating secondary structure.

(c) if your structure is from the Protein Data Bank, you may be able to also get the corresponding experimental electron density map and see how well it agrees with the coordinates in the PDB file. menu: File... Fetch by ID, database: EDS (2fo-fc), enter the same 4 digits as the PDB entry.  However, not all PDB entries have corresponding maps at EDS.

I hope this helps,
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 29, 2012, at 5:07 PM, rainy908 at yahoo.com wrote:

> Hi,
> I am new to Chimera.  I have a PDB of a protein comprising of a loop region that appears to have slight alpha-helical behavior when visualized in Pymol.  However, I doubt that this region is actually structured, and that this alpha-helical behavior is actually an artifact from experimental conditions.
> To double-check the validity of this loop, I was broadly advised that "crystal structure reconstruction" can be performed in Chimera.  I suspect this is either the 'molmap' or "Fit in Map" feature?
> Sincerely,
> Lili

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