Re: [ccp4bb]: physical meanings of positive and negative peaks in DANO Fouriermap

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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"Q. Steven Xu" wrote:
> 
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> I have two questions regarding the DANO fourier map.
> 
> 1) What's the difference between the maps calculated with
> coeff. F(+)-F(-) and with coeff. F(-)-F(+)? the postive and
> negtive peaks would be reversed?
> 
> 2) how to explain the positive and negative peaks in such a
> map? for instance, if I am searching a sulfur atom which produces the
> anomalous signal, I guess I need to search both the positive and negative
> peaks, is that right?
> 
> Thanks in advance.


 Aaaggh - you have uncovered an infelicity in the FFT implementation to
say the least..

 You MUST setDANO=DANO_whatever - the DANO setting flags that the input
phase must be advanced ( or is it retarded - check the documentation) by
90 degrees.

 Without that setting your maps will be garbage. 

 It isnt very logical I know.. we should change the system.

 But you dont need to check for both positive and negative peaks -
providing you didnt manage to mis-index the anomalous pairs andthat is
very difficult now with modern equipment..

My way of doing this is:
Use the GUI
Enter DANO=xxx PHI=PHI_mybestone W-FOM ( after a refmac run at present
you have to use CAD to merge the anomalous diffs and the PHIC/FOM from
the refinement) 

 I use the GUI to output a set of pdb peak list of "waters" from all the
Dano signals I have. 
Then add those to my coordinate file and look for close contacts - you
can use distang with RADI S 0.5 , O 0.5 and it finds which sulphur ( or
putative Na? CA? ) is near your peak list.

 Eleanor

> 
> regards,
> Q. Steven Xu

-- 
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Eleanor J.Dodson, York Structural Biology Laboratory,
                  Chemistry Department, 
                  University of York, Y01 5DD Heslington, U.K.
Tel: Work: +44 (1904) 32 82 53  Home +44 (1904) 42 44 49
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