Dear Tim,
In this case, I was using my anomalous dataset truncated at 5A resolution for
refinement and used Phenix to generate a Free R array:
Number of work/free reflections by resolution:
work free %free
bin 1: 49.6881 - 10.7634 [4605/4610] 4403 202 4.4%
bin 2: 10.7634 - 8.5575 [4565/4568] 4365 200 4.4%
bin 3: 8.5575 - 7.4799 [4588/4591] 4389 199 4.3%
bin 4: 7.4799 - 6.7979 [4592/4597] 4394 198 4.3%
bin 5: 6.7979 - 6.3117 [4616/4619] 4415 201 4.4%
bin 6: 6.3117 - 5.9402 [4582/4587] 4386 196 4.3%
bin 7: 5.9402 - 5.6431 [4589/4594] 4388 201 4.4%
bin 8: 5.6431 - 5.3978 [4567/4570] 4367 200 4.4%
bin 9: 5.3978 - 5.1902 [4572/4577] 4372 200 4.4%
bin 10: 5.1902 - 5.0113 [4621/4627] 4420 201 4.3%
overall 43899 1998 4.4%
I assume that if there is really twinning, one should choose rather more
reflections than less for the free R array to have around 5% for each twin
fraction?
Kind regards,
Hauke
-------------------------------------------------------
Hauke Hillen
Department of Molecular Biology
Prof. Dr. Patrick Cramer
Max-Planck-Institute for Biophysical Chemistry
Am Fassberg 11
D-37077 Göttingen
Germany
E-Mail: hauke.hil...@mpibpc.mpg.de<mailto:hauke.hil...@mpibpc.mpg.de>
Phone: +49-551-201-2864
On Oct 28, 2016, at 4:03 PM, Tim Gruene
<tim.gru...@psi.ch<mailto:tim.gru...@psi.ch>> wrote:
Dear Hauke,
when you use twin refinement, your R-factor is bound to drop whether it is
twinned or not. In your case Rfree rises, which is actually hinting at your
data not being twinned. How many reflections do you have in the Rfree set?
Best,
Tim
On Friday, October 28, 2016 1:59:29 PM CEST Hillen, Hauke wrote:
Dear Kay,
Thank you for your answer!
I have meanwhile processed my anomalous data also also as P1 and solved the
structure with MR-SAD in P1, which works flawlessly and gives the same
solution. Compared to P21, I now have 4 instead of 2 molecules in the ASU,
which makes sense. I then tried refinement in P1 with or without applying a
twin law in phenix.refine. The result seems very clear. Without twin law,
R/Rfree after one round of rigid body refinement drop to 34/38. With twin
refinement, the same refinement results in R/Rfree of 29/42. My current
suspicion is therefore that my data are truly P1, with an NCS axis parallel
to a crystallographic axis (suggested by Xtriage). Could this
pseudosymmetry lead XDS to falsely identify my data as P2 instead of P1?
Best wishes,
Hauke
-------------------------------------------------------
Hauke Hillen
Department of Molecular Biology
Prof. Dr. Patrick Cramer
Max-Planck-Institute for Biophysical Chemistry
Am Fassberg 11
D-37077 Göttingen
Germany
E-Mail:
hauke.hil...@mpibpc.mpg.de<mailto:hauke.hil...@mpibpc.mpg.de><mailto:hauke.hil...@mpibpc.mpg.de>
Phone: +49-551-201-2864
On Oct 28, 2016, at 3:51 PM, Kay Diederichs
<kay.diederi...@uni-konstanz.de<mailto:kay.diederi...@uni-konstanz.de><mailto:kay.diederi...@uni-konstanz.de>>
wrote:
Dear Hauke,
the conversion of intensities to amplitudes is an area with unsatisfactory
solutions, and the approaches of (and the assumptions made by) the
different programs differ. Low-resolution data are often anisotropic, which
adds difficulties. You could try CCP4 truncate/ctruncate and
GlobalPhasing's staraniso. The latter in particular should treat
anisotropic diffraction more properly. Probably you get yet other answers
from xtriage when fed with those amplitudes. Possibly this will add to the
confusion, but I'm not sure it is worth worrying about this too much.
Having said that, it seems to me like the primary and most unspoiled data
are the intensities. I don't see anything suspicious in the
xtriage-on-intensities output that you posted.
good luck with your difficult project!
Kay
--
--
Paul Scherrer Institute
Dr. Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297
GPG Key ID = A46BEE1A
