Hi Peter, Thanks for the reply. So not a bug, just a Really Undesirable Feature. I'm familiar with point group 32 and actually ran the program with both indexings, which unexpectedly came up with roughly the same R-free (irony: the incorrect indexing was marginally better). Mea culpa for not using my standard m.o. of comparing datasets using CCP4's SCALEIT. The reasons I consider this behavior to be a bad thing are: 1. Twin fractions > 0.5 are not physically reasonable and I would expect default behavior should be to clamp them to the range 0.-0.5. (caveat: I'm not sure what CNS or REFMAC do). 2. I have mixed feelings about "stealth reindexings", especially since I didn't set refinement.second_guess=True (see below) 3. The stealth reindexing behavior is inconsistent across refinement without twinning set (no stealth indexing) and when it is set, for exactly the same mtz and pdb files. Auto-reindexing might be a time-saving feature (especially in point group 3) but should be consistent w/ and w/o twinning enabled and needs to be much more prominently advertised in the output, and a new MTZ file written. Aside: this structure was the result of a MAD dataset at 3.5 Angstrom with a lower twin fraction (~0.2) so of course the relative indexing problem comes into play when I switched datasets. In the case of the MAD dataset SHARP made a radical difference in phase quality compared to the uninterpretable map straight out of SHELX - perhaps the largest improvement I have ever seen. Cheers Phil Jeffrey Peter Zwart wrote:

Hi Phil,

twinning with a twin fraction of 1-alpha is the same as twinning by alpha and reindexing your data (with the twin law for instance). Not a bug, but a consequence of structure solution, indexing ambiguities. Did you run MR, or did you have 'old' model already?

0.59 is the same as 0.41 (after reindexing), pretty close to the britton and H test (0.35). The ML test typically is lower then the other two estimates, as it tries to incorporate experimental errors.

HTH

Peter

2009/4/9 Phil Jeffrey :

...

While experimenting with twin refinement for a crystal in P321 that approximates P622 to varying extents, I noticed:

| twin fraction: 0.59 twin operator: -h,-k,l |

A bug, perhaps ?

This twin fraction would seem to be unlikely, since twin fractions > 0.5 have no meaning. Since this data does not scale well in p622 compared to some more heavily-twinned datasets on this xtal form I think the twin fraction is certainly less than 0.5.

Xtriage estimates: Statistics depending on twin laws ----------------------------------------------------------------- | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ----------------------------------------------------------------- | -h,-k,l | M | 0.150 | 0.343 | 0.347 | 0.283 | -----------------------------------------------------------------

Unless of course phenix.refine is reporting 2*alpha.

Phenix v1.4-3 Intel Mac OSX 10.5.6

This particular run with:

phenix.refine model-08.pdb pz7e_truncate-unique.mtz refinement.main.ncs=true strategy=individual_sites+group_adp --overwrite xray_data.r_free_flags.generate=True twin_law="-h,-k,l"

This is a very early non-finessed model.

Phil Jeffrey Princeton _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

Hi Phil,

The reasons I consider this behavior to be a bad thing are:

1.  Twin fractions > 0.5 are not physically reasonable and I would expect default behavior should be to clamp them to the range 0.-0.5. (caveat: I'm not sure what CNS or REFMAC do).

Twin fractions above 0.5 are physically reasonable! the twin fraction is the size of the twin domain. When you have a twin fraction of alpha, you always have a twin fraction of 1-alpha that goes with it. I wouldn't be surprised to see shelxl and refmac behave in a similar manner.

2.  I have mixed feelings about "stealth reindexings", especially since I didn't set refinement.second_guess=True  (see below)

I don't like a program to reindex data or model unless i ask to .

3.  The stealth reindexing behavior is inconsistent across refinement without twinning set (no stealth indexing) and when it is set, for exactly the same mtz and pdb files.

Auto-reindexing might be a time-saving feature (especially in point group 3) but should be consistent w/ and w/o twinning enabled and needs to be much more prominently advertised in the output, and a new MTZ file written.

no reindexing was done in phenix.refine. we could do so, but I have my reservations on that. Cheers P

Aside: this structure was the result of a MAD dataset at 3.5 Angstrom with a lower twin fraction (~0.2) so of course the relative indexing problem comes into play when I switched datasets.  In the case of the MAD dataset SHARP made a radical difference in phase quality compared to  the uninterpretable map straight out of SHELX - perhaps the largest improvement I have ever seen.

Cheers Phil Jeffrey

Peter Zwart wrote:

...

Hi Phil,

twinning with a twin fraction of 1-alpha is the same as twinning by alpha and reindexing your data (with the twin law for instance). Not a bug, but a consequence of structure solution, indexing ambiguities. Did you run MR, or did you have 'old' model already?

0.59 is the same as 0.41 (after reindexing), pretty close to the britton and H test (0.35). The ML test typically is lower then the other two estimates, as it tries to incorporate experimental errors.

HTH

Peter

2009/4/9 Phil Jeffrey :

...

While experimenting with twin refinement for a crystal in P321 that approximates P622 to varying extents, I noticed:

| twin fraction: 0.59  twin operator: -h,-k,l       |

A bug, perhaps ?

This twin fraction would seem to be unlikely, since twin fractions > 0.5 have no meaning.  Since this data does not scale well in p622 compared to some more heavily-twinned datasets on this xtal form I think the twin fraction is certainly less than 0.5.

Xtriage estimates: Statistics depending on twin laws ----------------------------------------------------------------- | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ----------------------------------------------------------------- | -h,-k,l  |   M  | 0.150  | 0.343         | 0.347   | 0.283    | -----------------------------------------------------------------

Unless of course phenix.refine is reporting 2*alpha.

Phenix v1.4-3  Intel Mac OSX 10.5.6

This particular run with:

phenix.refine model-08.pdb pz7e_truncate-unique.mtz refinement.main.ncs=true strategy=individual_sites+group_adp --overwrite xray_data.r_free_flags.generate=True twin_law="-h,-k,l"

This is a very early non-finessed model.

Phil Jeffrey Princeton _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

-- ----------------------------------------------------------------- P.H. Zwart Beamline 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 CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

this assumes two domains, right?  IIRC, every discussion of twinning i have read treats the problem in terms of two domains.  what is the basis for only having two domains (besides simplicity)?

The twin law is a rotation operator. the order of that rotation (2fold, 3 fold, 4 fold, 6fold) determines the number of domains for a single twin law.

someone mentioned a three-domain twinning problem (maybe ccp4 or phenix bb, last week or so) - wouldn't that need "1-alpha-(third domain fraction)"?

yes! P

-bryan

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-- ----------------------------------------------------------------- P.H. Zwart Beamline 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 CCTBX: http://cctbx.sf.net -----------------------------------------------------------------