Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's

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

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Subject: Re: pointless (1.2.0) and enantiomorphic SG's
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-11-09

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From: "Li, Yong" yol21 {- at -} PITT {- dot -} EDU
Date: 2007-11-09

Subject: Re: pointless (1.2.0) and enantiomorphic SG's
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-11-09

Merely encoding our state of knowledge of the space group into the file
header doesn't introduce any additional constraint. The very fact that
we are uncertain of the correct space group, whether or not that
information is encoded, is already a constraint on what operations can
be sensibly performed on the data.

The unit cell and indexing is uniquely determined by the Bravais lattice
assigned at auto-indexing time, except in the case where you have
already indexed another isomorphous (or near-isomorphous) dataset, and
the default indexing may not be what you want, so provided the Bravais
lattice has been chosen correctly then no re-indexing will be needed
when the space group is assigned. Provided you stick to the
conventional cell choice based on the Bravais lattice type, then the
selection of space group for a given Bravais lattice has no bearing
whatsoever on the indexing. Of course if you made the incorrect choice
of Bravais lattice originally, you're going to have to start over
anyway.

-- Ian

> -----Original Message-----
> From: owner-ccp4bb@jiscmail.ac.uk
> [mailto:owner-ccp4bb@jiscmail.ac.uk] On Behalf Of Kevin Cowtan
> Sent: 09 November 2007 14:52
> To: e.dodson@ysbl.york.ac.uk
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's
>
> Eleanor Dodson wrote:
> > Offering a selection of space groups compatible with a
> point group will
> > not require reindexing.
> > Some point groups of course permit reindexing, but one hope
> you have
> > chosen a consistent set as you combine data sets into an MTZ file -
> > pointless and the GUI both offer ways to check this.
> >
> > Phasing cannot be carried out till you have chosen a
> spacegroup, and any
> > existing phase associated data should probably be weeded
> out as part of
> > a "Assign Spacegroup" function.
>
> Good, that makes sense.
>
> Note however we have introduced a constraint on the data model:
> - Phasing and multiple spacegroups are inconsistent.
>
> Actually, IIUC, it's more complicated, since heavy atom
> location comes
> before phasing, but produces phases with enantiomorph ambiguity.
> Grahame's 4-step indicator of uncertainty provides the right sort of
> framework. But each step is associated with a corresponding set of
> restrictions on what is valid in the file - and in the case
> of phases,
> what they actually mean.
>
>

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CCP4bb navigation

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

Previous message:
Subject: Re: pointless (1.2.0) and enantiomorphic SG's
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-11-09

Next message:
Subject: POSTDOCTORAL POSITIONS
From: "Li, Yong" yol21 {- at -} PITT {- dot -} EDU
Date: 2007-11-09