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

[Harry Powell]

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
   <P 41 21 2> ( 92)    0.956  0.956                         00l: 
l=4n, h00: h=2n (zones 1,2)
   <P 43 21 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