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. > > ******************************************************************** > * * > * Dr. Manfred S. Weiss * > * * > * Team Leader * > * * > * EMBL Hamburg Outstation Fon: +49-40-89902-170 * > * c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 * > * D-22603 Hamburg Email: [EMAIL PROTECTED] * > * GERMANY Web: www.embl-hamburg.de/~msweiss/ * > * * > ******************************************************************** > > > 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 > > > > > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). 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