[Chimera-users] alpha helix representation problem

[Elaine Meng]

Hi,
We're glad you like Chimera!

The mutation and MD probably changed the conformation enough so that those residues are no longer automatically assigned as helix. Proline is sometimes considered a "helix breaker," so it is not surprising.

If you want to try running Chimera's helix/sheet identification method "ksdssp" with different parameter values, see the "compute SS" function in the Model Panel (which is in the Favorites menu): 
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
...or the command ksdssp:
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>

Or, if you are sure that you want these residues to be helix even if the calculation disagrees, you can manually assign them as helix.  There are several ways to do it, but here is one way:  First select the residues (you can do it by drawing a box in the Sequence tool), then click the green magnifying glass icon on the bottom right corner of the Chimera window to open the Selection Inspector.  In the Inspector, inspect "Residue" and change "in helix" to "true" (and "in strand" should be "false").

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 Oct 28, 2011, at 2:57 AM, larif sofiene wrote:

> greeting
> after a MD simulation of an in silico induced mutation A80P (located in an alpha helix) in a monomeric protein i get this strange alpha helix (a wire represented helix)
> http://imageshack.us/photo/my-images/573/alphahelix.jpg/
> is it the induced mutation that break down the alpha 3 helix and disturb orientation of the helix axis or a problem with chimera not recognizing the helix
> (in sequence tool the helix is no more color filled as alpha helix after inducing mutation)
> thank you for this piece of art which is CHIMERA :)
>