Hi Manfred
I agree with everything you say except the last bit about re-indexing!
For those space groups with alternate settings, e.g. those with standard
names C2 or P2221 or P21212, why is it necessary to re-index to the
'standard setting' when the data will have been already indexed
correctly by Mosflm or whatever according to the ITC Vol A convention
(e.g. a < b < c for the oI lattice)? It's not clear to me what you gain
by re-indexing in that situation (presumably at the heavy-atom solution
or translation function stage), and I know from experience that what you
lose is the risk of causing endless confusion by having datasets around
indexed in both ways.
This becomes particularly problematic when the data is stored in some
kind of database, because then you really want to have one definitive
space group name per crystal which is defined right at the outset and
cannot be changed. Changing the space group in mid-stream is then not
an option, except by deleting all the database entries for that crystal
and starting all over again with the new space group name. Of course if
the initial choice of space group was really wrong (e.g. the wrong
Bravais lattice assignment) then you have no option but to start over
and re-process the data.
The only other situation where re-indexing may be necessary is where you
know the correct Bravais lattice and approximate cell parameters
*before* processing the data, e.g. where you have a previously solved
isomorphous or near-isomorphous structure, but where the alternate
indexings have similar cell parameters so the initial automatic choice
of cell orientation may not have been correct.
Cheers
-- Ian
-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Manfred S. Weiss
Sent: 21 January 2008 09:34
To: Winter, G (Graeme)
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Spacegroup choices, reindexing and so on
Dear Graeme,
here is what I would do, or what I would like to have.
If you are able to identify the Laue group of the data with
some degree of certainty, then all of the processing and
scaling should be carried out in this Laue group.
Then, by looking at systematic absences you may give probabilities
for each of the possible space groups, i.e. each of the eight
possibilities in P-orthorhombic. Typically one option will
have the highest probability and this is the one which should
be written out. In a second run, the user should be given the
choice of overriding this.
Now, for space groups such as P222_1, this should always be
reindexed to standard setting, if it turns out to be the one
with the highest probability.
Hope that helps,
Manfred.
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On Mon, 21 Jan 2008, Winter, G (Graeme) wrote:
Hi All,
A user question about the xia2 behaviour has opened a pot
of worms, and
I thought I would ask the community for opinions. If (for
example) you
are using an automated data processing or analysis tool, and the
systematic absences suggest a spacegroup choice, what would
you like to
do:
(1) nothing - just mention this in the output
(2) assign the "base" version of this spacegroup (e.g. P41212 to
represent that or it's enantiomorph)
(3) create multiple copies of the reflection file with all of the
spacegroup options
As a further question, if the spacegroup looks like P 2 21 21 (say)
would you like this to be reindexed to the standard setting?
Now, I suspect that there will be a wide range of opinions on this.
Following #1 will give possibly strange effects if truncate tries to
inflate systematically absent reflections
Following #2 will result in reflections being removed by truncate
#3 gives lots of reflection files and lots of mess
Currently I follow #2 with reindexing to the standard setting.
There have been discussions in the past of being able to flag "or
enantiomorph" in the spacegroup definition in the mtz file.
This would
be useful here, but would not really help with the reindex or no
question...
Thanks!
Graeme
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