[Chimera-users] crystal structure reconstruction

[rainy908 at yahoo.com]

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


On 30 September 2012 10:47, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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.)
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html>
>
> 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.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
>
> (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.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html>
> <http://eds.bmc.uu.se/eds/index.html>
>
> I hope this helps,
> Elaine
> -----
> 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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