Re: [sdpd] McMaille slight update

[Armel Le Bail <alb...@cristal.org>]

>Is there any chance that McMaille could be modified to have a scale
>factor - to do all the scaling internally rather than manual changes
>to the values (sort of how Crysfire works)?

Well, being included in the next Crysfire release, McMaille
automatically benefits from the Crysfire rescaling system, if
McMaille is activated inside of Crysfire.

>Plus for black box mode - could this be part of the search strategy -
>autorescaling procedure based estimated volumes to maximize a chance
>of getting a good solution for large cells?  (is there any reason
>why proteins could not be indexed in black box mode?)

I have tried the tetragonal lysozyme data from Bob Von Dreele,
available in your talk (Korea, 2002) at CCP14 :
http://www.ccp14.ac.uk/poster-talks/korea_2002c/sld040.htm

By manual rescaling in black box mode (changing the wavelength
to 0.115006 instead of 1.15006 A), the tetragonal solution is not
found. An orthorhombic cell is proposed with a~b which can
allow to guess the tetragonal cell, the profile reliability factor is 13%,
suggesting that the data quality is not high (but this is relative
since the R factor is dependent of the selected peak width -
enlarging the peak width reduces Rp).

The tetragonal cell is found then in manual mode by enlarging
the peak width to 0.050 (°-2-theta) instead of the 0.022 value
suggested by the software itself. That peak width suggestion is
calculated by an empirical formula : 0.30*lambda/1.54056 (so as it is
0.30 for Cu Kalpha).

So, clearly, rescaling should be applied not only to the wavelength
but also to the peak width for having a chance to index a protein in
black box mode with McMaille.

This is not a problem to modify McMaille with a correction
of the peak width empirical formula for very short pseudo-wavelengths
in automatic mode. Decreasing artificially the wavelenght unfortunately
does not improve the data quality...

But how many crystallographers are indexing proteins from
powder data ? They have to be experts in crystallography I guess,
and will not be repelled by manual modes (putting hands in grease =
"mettre les mains dans le cambouis" in french ;-).

Armel

PS - Carlo U. Segre has made a Linux Debian package of McMaille,
thanks !             http://www.iit.edu/~segre


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