[Xplor-nih] Left handed residue in Ramachandran

[John Kuszewski]

Hi,

You're right that the left-handed helix is a small minimum in the  
Ramachandran plot.

In calculating structures with limited experimental data + repulsive  
vdWs, you
do see an unusually large number of residues in the left-handed  
helix.  That's largely
caused by the relative inaccuracy of the repulsive vdW potential.

The best way to correct this is to use xplor-nih's RAMA potential in  
addition to the experimental
data & repulsive vdWs.  The RAMA potential pushes rotatable bonds  
toward physically reasonable
combinations, with lower energies for more-commonly seen combinations  
of torsion
angles (i.e., the right-handed helix has a much lower RAMA energy  
than the left-handed helix).

Examples of its use are in

xplor/eginput/gb1_rdc/anneal.py  (for Python)
xplor/eginput/marvin/cvn/sa_pass2.tcl (for TCL)
xplor/eginput/fbp/domain2_tor_final.inp (for classic xplor)

If you want background information, I had a couple of papers  
describing the technique:

Prot Sci 5: 1067 (1996)
J Magn Resn 125: 171 (1997)
J Magn Resn 146: 249 (2000)
J Am Chem Soc 124: 2866 (2002)

Hope this helps.

--JK

On Apr 18, 2007, at 10:31 AM, Shi,Lei wrote:

> Hi groups,
>    I am using Xplor-nih to refine a small protein with two helical  
> domains
> and a loop connecting them. I am using NOE restaints and torsion angle
> data.
>    When I analyze the final structure, I found that there are 1-2  
> residues
> in the left hand helix region in the Ramachandran plot for a  
> overall of
> around ~50 structure. I use torsion angle dynamics and only use the
> replusive vdw potential.
>    I do not have a lot of restraints in the loop region. I do not know
> whether it is the reason I have those left handed helix. It is rare  
> to see
> the left handed though.
>    I do not know what I might have done wrong. Any help is greatly
> appreciated.
>    Thanks,
>    Lei
>
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