Re: [ccp4bb]: averaging

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

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Bernhard Rupp wrote:
> 
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> Dear All:
> 
> Gokulan and I are stuck with what ought to be a simple procedure (harhar)
> Given: a h k l fo, fom, phwt file, warped from a trimer w/o using NCS
> Wanted: a 3-fold averaged map with NCS, in hope to improve weak density.


 NCS operators are hateful things.. 

 All I know is that CCP4 programs are at least internally consistent so
that it is worth checking the matrices with lsqkab.

 I presume you want to average over the B molecule?

 So I would run 
lsqkab xyzinw ABC.pdb xyzinr ABC.pdb
fit wres 1 to 999 wch B
match rres 1  to 999 rch A
end

Ditto B to C
Then check whether the rotation matrices are  the one you have from CNS

Alternative, often better..
 If you have 3+ heavy atom sites per monomer  I would prob. start from
the matrices they generate and use dm with AVER to refine the fit
against the exptl phases..
 
> Succeeded:
> make a ccp4 map (awk, fft)
> make a cell map (mapmask)

 f2mtz fftbig will give you the whole unit cell.

> make a xtalview map (map2fs, thanks Frank!)
  Can do this from the ccp4i GUI 

> rtftm maprot (t for thin)


 Which version do you have? It was upgraded somewhat..


> used NCS ops from CNS (probably questionable as the rmsd is 4.5A)
> nevertheless, script made and resulting map has no overlap according
> to log.
  Hmmm - 4.5A is a big deviation..
By the way - where did CNS come into this? 

> Inspection of input maps satisfactory.
> Transposition of matrix gives same nonsense. Maps look unchanged from input
> map.
> 
> I guess the result is Bad news:


 Looks like it!

 Eleanor