Bernhard

There's the related issue of how to optimally treat the *test set*
reflections, i.e. perfectly good measurements but not used (in
refinement that is).  The various program authors seem to treat these
quite differently, e.g. Refmac AFAICS treats them exactly like
unobserved for the maps and sets FOM=0, FWT=DFC, DELFWT=0.  Buster
AFAICS assigns a FOM>0 and treats them just like normal reflections for
the maps.  I don't quite understand why Refmac can't assign a valid FOM
in this case, since that's obtained from the calculated phase
distribution, and AFAICS has nothing to do with whether or not the
reflection is used in refinement.  I've no idea what Phenix does in this
situation.  It would be nice to have some transparency/consensus on best
practice!

There's also the issue I highlighted in January on the BB where none of
the programs I tested (Refmac, Buster) were using the correct formulae
for FWT in the centric case, or DELFWT in one or other of the acentric
or centric case (apologies to Garib if his latest version fixes this, I
haven't had time to test it yet).

Cheers

-- Ian

> -----Original Message-----
> From: [log in to unmask] [mailto:[log in to unmask]]
On
> Behalf Of Bernhard Rupp
> Sent: 18 March 2009 01:34
> To: [log in to unmask]
> Subject: map coefficients for padded reflections Fobs=0
> 
> Dear All,
> 
> 
> 
> during processing some mtz files I noted that some programs complete
> 
> the reflection list by padding missing reflections.
> 
> 
> 
> a)      for Refmac (which did not pad reflections automatically) I
read
> that
> 
> 1)      for 2mFo-DFc:  Fwt = DFc in case Fo=0
> 
> 2)      for  mfo-fc :       Fwt=0 for Fo=0
> 
> 
> 
> b)      how does PHENIX/refine handle the fobs = 0 reflections in
either
> case?
> 
> 
> 
> c)      Prime and switch maps also have padded reflections, but here I
am
> at a loss,
> 
>             because the maps seem to acquire very high positive
density -
> i.e. the distribution
> 
>             seems atypical when read into say Xtalview. Might be a
result
> of the density modification
> 
>             procedure? Can I get the observed reflections only from
P&S?
> 
> 
> 
> Could the program authors kindly shed some light or references on the
> treatment of absent reflections in their
> 
> respective programs? In most cases, the padded reflections have not
much
> effect, as expected from their weights.
> 
> 
> 
> Thx, br
> 
> 
> 
> Bernhard Rupp
> 001 (925) 209-7429
> +43 (676) 571-0536
> [log in to unmask]
> [log in to unmask]
> http://www.ruppweb.org/
> -----------------------------------------------------------------
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> The few who make things happen
> The many who watch things happen
> And the overwhelming majority
> who have no idea what is happening.
> -----------------------------------------------------------------
> 
> 



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