Re: [ccp4bb]: Phasing Phoiled by Phistats in Philadelphia. Pfui.

[Bart Hazes <bhazes@ualberta.ca>]

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SFTOOLS has an option specially for this situation. It is called PHASHFT and
you only have to tell it which two columns to compare. It can print the phase
difference in either degrees or as a figure of merit and it will give the
stats as function of resolution. E.g. (assuming the phase columns have labels
phi1 and phi2):

sftools
yourfile.mtz
phashft col phi1 phi2
stop

Phoila...

Bart

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
> 
> 

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