[Chimera-users] helix anomaly

Elaine Meng meng at cgl.ucsf.edu
Fri Dec 9 11:41:52 PST 2011

Hi Larif,
Different programs use different methods for identifying helices and strands, so it is not surprising that the results are sometimes different. It does not mean there is a bug.  

The "ksdssp" method used by Chimera is described here:

If you want that final turn to appear as helix-type ribbon in Chimera, you can either (a) re-run the ksdssp calculation with different settings to see if it gives what you want, or (b) simply assign those residues as helix manually without running a calculation.

(a) To try recalculating with different ksdssp parameters, you could use the "compute SS" function in the Model Panel (Favorites... Model Panel in menu), or the command "ksdssp."

(b) To reassign manually, you could use the Selection Inspector or the command "setattr."  Selection Inspector: select the residue(s), open the Selection Inspector (by clicking the green magnifying glass on the bottom right corner of the Chimera window), change to Inspect "Residue," and then set the "in helix" and "in strand" true/false attributes as desired.  Command "setattr" example:

setattr r isHelix true :184-190

to assign residues 184-190 as helix.

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 Dec 9, 2011, at 11:18 AM, larif sofiene wrote:

> Greeting sir
> I'm studying a protein mutation effect using M.Dynamics, and when got results a used chimera to view my protein.
> in this snapshot http://imageshack.us/photo/my-images/839/errya.jpg/ you can see the first arrow (helix distortion, which predicted as a mutation effect ) and a second arrow showing the discontinuity the helix,where its final turn is replaced by a coil.
> My question is this coil a secondary structure detection bug in chimera,because when using other tools (pymol, vmd ) they detect this final coil as a helix.
> thanks

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