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Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: pointless (1.2.0) and enantiomorphic SG's From: Harry Powell harry {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK Date: 2007-11-09 Of course, you may need to re-index even if you have the right space group... > 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. > > > Eleanor > > > > Kevin Cowtan wrote: >> This is great! But before we all get carried away, a quick reality >> check is in order. This isn't an area I've thought about, but my >> limited understanding raises the following issues.... >> >> Given that an MTZ file contains a cell, an indexing of the data, and >> possibly phases involving a choice of origin, the use of an MTZ file >> immediately implies that some decision has been made about the >> spacegroup. >> >> Selecting a different spacegroup from a list of possibilities may >> involve reindexing, and/or changing origin/enantiomorph dependent >> properties such as phases and HLs. >> >> It would be possible for an MTZ file to say something like this: >> 'This file is generated assuming spacegroup X. Spacegroups X1, X2, >> X3, X4, X5.... are also possible.'. >> >> It should also be possible to compute on the fly whether a particular >> column type needs to be modified for a different spacegroup. >> >> How will we present this in user interfaces? As a starting point, >> until a spacegroup has been settled upon, the user will need the >> option of picking the spacegroup after having selected the MTZ. This >> means potentially a reindexing step added to every single task - >> messy. As an intermediate, being able to change the 'currently >> selected' spacegroup as a separate task would be an improvement. >> >> >> Phil Evans wrote: >>> I agree >>> >>> On 9 Nov 2007, at 13:50, Eleanor Dodson wrote: >>> >>>> As I often say!!! The mtz format should carry point group and >>>> alternate SGs - then be upgraded when youknow the correct SG.. >>>> >>>> Eleanor >>>> >>>> Phil Evans wrote: >>>>> It just picks the first in the list, to store in the output MTZ >>>>> file, which can only handle one (92 < 96) >>>>> Phil >>>>> >>>>> >>>>> On 8 Nov 2007, at 22:26, Bryan W. Lepore wrote: >>>>> >>>>>> when pointless (1.2.0) finds enantiomorphic SG's, what is the >>>>>> criterion for 'Selecting' one over the other? >>>>>> >>>>>> e.g. i ran pointless on some tetragonal data, and the >>>>>> enantiomorphs SG92/SG96 are selected as strong candidates >>>>>> >>>>>> Spacegroup TotProb SysAbsProb Reindex >>>>>> Conditions >>>>>> ( 92) 0.956 0.956 00l: >>>>>> l=4n, h00: h=2n (zones 1,2) >>>>>> ( 96) 0.956 0.956 00l: >>>>>> l=4n, h00: h=2n (zones 1,2) >>>>>> >>>>>> ... then pointless reports : >>>>>> >>>>>> Selecting space group P 41 21 2 as solutions are enantiomorphic >>>>>> Best Solution space group P 41 21 2 >>>>>> >>>>>> ... is that b/c pointless can only report one, and SG92 came up >>>>>> first? >>>>>> >>>>>> -bryan >>>>> >>>>> >>>> >>> >>> >> >> CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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