Hi Xiaofei,
You might want to try the backrub tool in KiNG
(http://kinemage.biochem.duke.edu/software/king.php) .
This allows one to make subtle correlated changed along the mainchain,
and watch the effect on the fit to the Ramachandran plot.
Richardson Lab
Duke University
On 8/3/07, Xiaofei J
Every modern structure should be "above average" by procheck criteria.
For modest resolution structures, the availability of ncs restraints
should have a big effect on one's Ramachandran expectations: I've
found ncs restraints at 3-3.5A do wonders for the Ramachandran plot
even when they don't
Dear all,
I am now preparing my structure for deposition. The
crystal diffracts to 3.0 A. R: 0.20; R free: 0.25.
What I am concerned with is the Ramachandran plot;
83.5% in core region, 15.8% in allowed, 0.5 % in
general allowed,0.2% in disallowed region. The model
fits in density pretty well an
Procheck puts out such a correlation (% most favorable
vs resolution) in the _04.ps file. For example look at
page 7, first panel of the sample procheck output at:
http://sb20.lbl.gov/SQR/procheck-2H88.pdf
It appears that 83.5% would be well above average
for a 3 A structure according to procheck
