[phenixbb] twin/pseudo-symmetry question

Peter Zwart PHZwart at lbl.gov
Fri Nov 11 10:28:51 PST 2011

Hi Todd,

There are 3 possible C2's you can choose from. Try besides R32

C2 (no 1)
C2 (no 2)
C2 (no 3)

If you use labelit / imosflm you have full control over which
spacegroup you can choose. HKL2000 doesn't provide enough control over
which indexing solution you want to use.

Alternatively, you could have an 'obverse/reverse twin' in R32, a
special kind of reticular twin. In this twinning form, the hexagonal
sublattice causes the twinning. When you index your data, check if the
integral absences are indeed absent (when you are in the hexagonal
setting). If not, you could have an obverse reverse twin.

I have no clue about CCP4, but in phenix selecting the free set is
done properly using the full symmetry of the lattice. If this is done
incorrectly, you will get in trouble later down the line, so better
make sure that things are ok.


On 11 November 2011 10:03, Green, Todd <green at cbse.uab.edu> wrote:
> For the R32 set, I generate the r-free in phenix directly from the scalepack file for data processed in R32. For C2, it was generated from the C2 processed scalepack file but in ccp4 using the scalepack2mtz script then imported to phenix(because i used molrep for the molecular replacement). But, I kept this same data file with the same r-free for all of the refinement runs before and during twin refinement. Seem reasonable?
> -Todd
> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org on behalf of Nathaniel Echols
> Sent: Fri 11/11/2011 11:53 AM
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] twin/pseudo-symmetry question
> On Fri, Nov 11, 2011 at 9:47 AM, Green, Todd <green at cbse.uab.edu> wrote:
>> the true space group is C2. Are these r-values too low? does the difference
>> in values according to each twin law mean something?
> I don't know enough to answer the rest of the question, but one thing
> to look out for is how you generate the R-free flags - which program
> did you use, and when you reprocessed in C2, did you generate a new
> set of R-free flags?  If you're not careful with this, you can end up
> severely biasing R-free when performing twinned refinement.
> -Nat
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P.H. Zwart
Research Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:      http://bcsb.als.lbl.gov
PHENIX:   http://www.phenix-online.org
SASTBX:  http://sastbx.als.lbl.gov

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