[ccp4bb]: M.R. woes

[David Mandelman <dmandelman@nethere.com>]

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>when i do a cross
> rotational search, going by the rotation function peak height
> values it seems
> to have worked. (highest values are .1591 and .1496 and the
> rest of the values
> are in the .06 range).


Cheenu,


Based on your cross rot. results, it is possible that you have 2 mol.'s
in the asymmetric unit (A.U.) run thru a quick Matthews calc (Vm) to
figure out the number of mol.'s in the A.U.  To do this:

Vm = (A*B*C)/(4*M.W.*Z)

A,B,C are your unit cell lengths
4 is the number of symm op.'s for the orthorhombic space group
M.W. is the mol. weight of your molecule
and Z is the unknown number of mol.'s in the A.U.

You supply values of Z until your Vm falls between 1.7 - 3.5, a typical
value for most proteins.  Of course, not all prots will fall in this
range, but if you find a value of 2, then you may want to look for a
second molecule in the A.U., you already have the rot. sol'n. for it.

Otherwise, It sound like if you have a high signal above background for
you translation search, then you found the rot/trans function for your
M.R.  But, make sure you then PROPERLY apply this sol'n to your original
model. For example, pre-GUI-CCP4, required that the rot/tran sol'ns be
modified by certain values (center-of-mass and a rotation value)
established early on in the M.R. The original search model was then
rotated and translated by these values and then CNS refinement could
begin. I am not familiar with M.R. in CNS, so you may want to have a
look at the tutorials regarding this, otherwise, try AMORE in the new
CCP4 package, the GUI interface makes things easy.

Anyhow, those are just a couple of suggestions, good luck.

Dave M