PHabulously-PHriendly PHrequently-PHrostbitten PHortran PHringe-PHossil PHinds PHormidable PHrigging PHrightening PHrivolous PHundamental PHunctional PHormula PHalsehood (Re: [ccp4bb]: Phasing Phoiled by Phistats in Philadelphia. Pfui.)

["Gerard \"DVD\" Kleywegt" <gerard@xray.bmc.uu.se>]

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To Pat the PHantom PHarmacologist-turned-programmer, PH.D.:

I don't know about PHISTATS, but just mapping your
PHase angles to a PHixed interval (0 to 360 or -180
to 180) isn't necessarily good enough. PHor instance,
iPH PHI1 = 357 degrees and PHI2 is a dirty ol' 3
degrees, you will calculate a diPHPHerence oPH 354
degrees, whereas in actual PHact it is a mere 6 degrees
oPH Kevin Bacon (modulo sign).

So, to calculate the absolute diPHPHerence, you should
do something like this (assuming you program in PHortran;
iPH not, let me know and I'll send you a PHlow-diagram):

      diPH = abs (phi1 - phi2)
      if (diPH .gt. 180.0) diPH = 360.0 - diPH

On a more PHilosoPHic note - I PHear that:

>Of course one might suspect the little program I've written; but I've
>checked it every way I can imagine; and I think that even my meager coding
>skills are up to the task of calculating a difference between two columns
>of numbers and then averaging it...

is an - how shall I PHrase it - amusing example oPH
"PHamous last words" that will probably haunt you PHor
years to come. Maybe it's time to emigrate to PHlorida
or even, God PHorbid, PHrance ?


--Dr Quasi-evil




On Thu, 8 Feb 2001, Patrick J. Loll wrote:

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> ***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***
> 
> I'm confused about output I obtain from phistats.  I'm attempting to
> calculate the phase errors associated with various phasing procedures.
> I've written a little program to calculate the quantity:
> 
> <|deltaPhi|> = the mean value over all reflxns of the absolute value of the
>                difference between Phi1 and Phi2.  I calculate this for all
>                reflxns and for acentrics only
> 
> In all cases, the DELF number obtained from phistats (described in the
> output as "average difference in degrees" for acentric reflxns) is
> substantially lower than the number I calculate independently (by, say, 20
> degrees).
> 
> I've tried all the controls I can think of.  The most stringent control was
> to write h, k, l, F, sigF, Phi1, & Phi2 into a single ASCII file, one line
> per reflxn.  I made certain Phi1 and Phi1 both lay between 0 and 359 deg
> (ie, not -180 to 180).   I can then use F2mtz to create an mtz file from
> this & feed it into phistats.  This should cover most of the obvious
> problems (eg, reflxns from different sources reduced to different asym
> units).  The problem still persists.
> 
> I'm assuming DELF is equivalent to quantity I describe above.  Am I wrong?
> I think it should mean the average absolute difference, rather than  the
> "average difference," since the phase errors are uncorrelated, and over a
> large dataset will average to zero.
> 
> Of course one might suspect the little program I've written; but I've
> checked it every way I can imagine; and I think that even my meager coding
> skills are up to the task of calculating a difference between two columns
> of numbers and then averaging it...
> 
> 
> 
> Pat, Puzzled in Pennsylvania
> 
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> 
> Patrick J. Loll, Ph. D.                             (215) 898-1294
> Department of Pharmacology                     FAX: (215) 573-2236
> University of Pennsylvania School of Medicine
> 3620 Hamilton Walk
> Philadelphia, PA  19104-6084  USA
> 
> loll@pharm.med.upenn.edu
> http://pharm.med.upenn.edu/Loll/loll_lab.html
> 
> 
> 

******************************************************************
                        Gerard J.  Kleywegt
Dept. of Cell & Molecular Biology  Bolshevik University of Uppsala
                Biomedical Centre  Box 596
                SE-751 24 Uppsala  SWEDEN

    http://xray.bmc.uu.se/gerard/  mailto:gerard@xray.bmc.uu.se
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