Re: [ccp4bb] difficult MAD dataset

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: correlation length - reloaded
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2009-02-03

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Subject: Re: difficult MAD dataset
From: "Stephen Graham stepheng {- at -} strubi {- dot -} ox {- dot -} ac {- dot -} uk
Date: 2009-02-03

Subject: Re: difficult MAD dataset
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-02-03

Hello -

Sorry if some of my suggestions are redundant since I jumped in late
in this thread.

A couple of additional comments after struggling with a similar albeit
not identical case.

> With a pseudo translation vector like that the SG could be any of
> the 8
> orthorhombic SGs; P222 P21 22 P21212 P212121 P2 21 2 P2 21 21 P 2 2 21

In addition to these, I would also examine lower symmetry space groups,
namely the three P21, where each axis is considered successively
monoclinic. (see below)

>> Chi2 is unusually high at lower resolution (Chi2 is >3 from 3.5A as
>> shown
>> below) and there is a relatively high percentage of rejections
>> (>1.5 %).

Chi^2 in Scalepack *must* be adjusted by changing the expected errors
to be about 1.
Until then, I would not reject reflections. Only then I would reject
reflections and then readjust chi^2 to be 1 again.
Having said that its quite a while since I used scalepack.
Maybe in the age of automation scalepack does this now automagically
in the context of HKL2000, but a Chi^2 of 3
at low resolution indicates that some reflections and very likely
their sigmas do not have realistic intensities, and also
that your rejections might be excessive.

Moreover, given the apparent very high quality of your data (it goes
far beyond 2.5 A !!!), I would had expected
lower Rsym at low resolution (from a good beamline or home source).
Thus I would be skeptical about the
symmetry.

I would process the data at P1 and then either let Pointless or X-
triage suggest the Laue group for the scaling.
Both give truly informative and clear statistics for the Rmerge upon
the introduction of symmetry elements
and for the space groups. (btw these two programs are so brilliant. It
was taking me ages to try scaling in alternative space groups
by hand in the past - reminder: free beer to Phil and Peter for the
2009 meetings!) ;-)

Good luck -

Tassos

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: correlation length - reloaded
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2009-02-03

Next message:
Subject: Re: difficult MAD dataset
From: "Stephen Graham stepheng {- at -} strubi {- dot -} ox {- dot -} ac {- dot -} uk
Date: 2009-02-03