Re: [ccp4bb]: M.R. woes

[Anastassis Perrakis <perrakis@nki.nl>]

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> 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.

Or, simply, click at ccp4i the button 'Cell contents nalysis' and give the
mtz file name and the MW of the protein !

>
> 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.

Again in ccp4i, when you run molecular replacement programs there is a
button provided for the
case that Frank and Fred have cunningly spotted, i.e. that the 'space group
hypothesis' is wrong.
You can use ccp4i very easily to try all P-orhtorhombic hypotheses, i.e.
P222, P2122, P2212, P2221,
P21212,P22121,P21221,P212121. That might be usefull especially in cases that
one of the axes of
the crystal was perfectly aligned with the spindle in data collection and
you miss all h00/0k0/00l reflections
and can not decide really if there is a screw axis or not.

I also cannot help the personal bias, i.e. suggesting to run arp/warp on
molecular replacement solutions
if data are in a descent resolution: 2.0 A or better for autobuilding, or
2.0-3.0 for just 'model update'
combined with refmac refinement. And dont forget 'resolve' for 'prime and
switch' - it tends to give
nice bias-reduced maps from molrep solutions.


    Tassos


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