>
> Ian,
>
> I agree with your description, but not quite with your
> conclusion. In the
> original poster's problem one of the cell axes is so short
> that at most a < 20
> Angstrom Patterson outer radius can be used in a
> Patterson-based rotation
> function. This will inevitably lead to loss of many
> interesting Patterson
> vectors, and probably a low signal-to-noise ratio.
>
> So in this particular situation the "direct rotation function"
> (http://dx.doi.org/10.1107/S0907444995001284) might have a
> distinct advantage
> compared to Patterson methods, which is why I suggested it.
> Whether this is
> enough to solve Pietro's problem remains to be seen. For me
> it's a case of "know
> your options, and try them".
>
> best,
>
> Kay
>
> --
> Kay Diederichs http://strucbio.biologie.uni-konstanz.de
> email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183
> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
>
Kay,
But there's nothing in say AMoRe to stop you increasing the radius cutoff to
whatever is required to optimise the signal/noise ratio, apart from this silly
IF statement which I always used to delete (I just commented out the CALL
CCPERR statement):
ELSE IF (RMAX.GT. AOBS .OR. RMAX .GT. BOBS.OR. RMAX.GT.COBS)
+ THEN
WRITE (6,*) 'Radius: ',RMAX, ' Cell: ', AOBS,BOBS,COBS
CALL CCPERR(1,'Sphere radius > cell edge')
There's also a program limit in AMoRe on the ratio
radius-cutoff/high-res-cutoff due to max Bessel order but since this is
currently 500 there will be few cases where it's a limit in practice (it's ~
80, so max 200 Ang radius for 2.5 Ang data). There's obviously no point in
having a radius cutoff bigger than the greatest molecular diameter (there are
no intra-vectors longer than this).
Some people object to including the transform of the origin peak vectors in
adjacent cells, but the direct rotation function is effectively doing just that
and no-one complains (as long as it solves their structure)! It seems to me
it's particularly important to perform this radius optimisation for highly
ellipsoidal molecules, because as you point out a limit of 20 Ang with a
molecule 100 Ang long will only include a small fraction of the intra-vectors.
There will always be a trade-off between increasing the number the
intra-vectors thus improving the signal, and increasing the number of
inter-vectors thus increasing the noise. It's just a question of finding where
the optimal radius cutoff giving the maximum signal/noise ratio lies.
The direct rotation function sometimes used to work better than the
Crowther-type function not so much due to the lack of radius cutoff, but more
because 1) it uses E's not F's; 2) it uses a correlation coefficient function
rather than a product function (the latter is much easier to code using FFT's);
3) the radius cutoff for the Crowther function was often not optimised; and 4)
care wasn't taken not to lose strong reflections at low res which several
people have demonstrated has a disastrous effect on F-based functions, but is
less critical with E-based functions. However use of a correlation coefficient
function based on E's is now a feature of AMoRe (if not the CCP4 version then
Jorge Navaza's version).
Anyway this is all academic now, I always use Phaser which does all this
properly (I have no experience using it for highly ellipsoidal models though).
Cheers
-- Ian
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