[sharp-discuss] automatic MAD wavelength analysis confusion

[Clemens Vonrhein]

Hi Roni,

the 'problem' is that within autoSHARP we have two systems in place:

  - SHARP needs to know the f'/f" values of the heavy atoms
    (obviously) to do the refinement and phasing

  - SHELXC/SHELXD wants to know the 'names' of each dataset (PEAK,
    INFL, HREM, LREM) (presumably to translate these into some magic
    relation between the underlying f'/f" values ...)

So autoSHARP needs to keep track of both. In a good MAD experiment we
will have the situation that

  - peak has the largest f" value

  - infl has the lowest f' value

 - lrem/hrem are collected so far away from the edge, that the
   calculated values (via CCP4's CROSSEC program) are more or less
   correct

What happens often is that e.g. the lrem/hrem are collected 'just
remote enough' (but still fairly close to the calculated edge for
agiven element): this would confuse autoSHARP.

Or in your case it seems that you gave

  peak : f' = -8.0266  f" = 3.8421
  inf  : f' = -9.8034  f" = 3.8438

So here the 'inf' dataset has the lowest f' _and_ the highest f"! If
you want to give typical values I would do:

  peak : f' = -6.0  f" = 6.0
  infl : f' = -8.0  f" = 3.0
  hrem : f' = -1.5  f" = 3.5
  lrem : f' = -2.0  f" = 0.5

(or something similar). 

However, there is a little 'trick' (or maybe you could call it a
work-around) on top of these 'typical' values: give your wavelengths
some meaningful identifer ('peak', 'infl', 'hrem', 'lrem'). Then
autoSHARP should use those identifiers at the SHELXC/D stage - to keep
these programs happy.

Obviously, the fluorescence scan or jotted down numbers for f'/f"
would be best ;-)

Cheers

Clemens

On Tue, Aug 21, 2007 at 11:00:28AM -0400, Roni Gordon wrote:
> Hi all,
> 
> Just trying to re-process MAD data without the accompanying fluoroscence
> scans... I tried using "typical" values for peak & inflection (0.97924
> and 0.97940 A), and I was surprised when autoSHARP choked.  
> 
> Upon further inspection, both wavelengths were assigned a value of
> "peak" which was a problem for SHELX.  The following output was
> obtained:
> 
> 
>  WARNING : the identifier (peak) seems to suggest a peak wavelength, but the MAD
>            analysis results in assigning it as "inflection". We will be using the
>            user-defined assignement as "peak"!
> 
>              wavelength 1 (peak: 0.97924 Å with f'= -8.0266 f"=  3.8421 for Se) = peak
>              wavelength 2 ( inf: 0.97940 Å with f'= -9.8034 f"=  3.8438 for Se) = peak
> 
> The inflection is presumably still a few eV below the peak at this
> longer wavelength, and yet the tables still suggest a higher f''?
> 
> Any insight into this confusing (but I'm sure simple) matter would be
> greatly appreciated.
> 
> Roni
> 
> 
> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss at globalphasing.com
> https://www.globalphasing.com/mailman/listinfo/sharp-discuss
> 

-- 

***************************************************************
* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group      (http://www.globalphasing.com)
***************************************************************