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1) You should use measured data (after scala/aimless/truncate). In general there may not be one to one relationship between observed data and asymmetric unit (e.g. non-merohedral twinning) and it would not be possible to bring input data to output file. Use original data
2) Internally refmac groups reflection into classes. All twin related reflections belong to one class. In the example you give four reflections belong to one class. FreeR is property of the class not individual relfections. I.e. all twin related reflections belong either to free or working class. If your input data has this property then output should also have this. In the output file there will be 0 (for free) and 1 (working)
3) At early stages it is not easy to factorise twin and underestimated symmetry. It seems that L-test is the best way of making decision if you "crystals" are twinnined. If you collect data from many crystals and merge them then you artificially twin (or increase twinning). Using pointless to index all datasets consistently may sort some of the problems 
4) In this case it seems that you may need to reindex. Largest twin domain is not the first one

Regards
Garib


On 2 Mar 2012, at 02:00, wtempel wrote:

Dear CCp4ers,
A good morning to everyone.
Today, I have a structure that I initially refined in space group P6522, 1mol/asu.
Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; <I>/<sigma> > 3
2.61-2.55A: Rsym=39.6%, <I>/<sigma> > 10
50.00-6.13: Rsym=6.4%
Some mild anisotropy in the resolution limits is apparent on the diffraction images. Say, visible spots at 2.2A in one direction, 2.6A in the other.
Rfree, using data to 2.3A, was stuck in mid-30%s. The map appears like 3.5A resolution, with some difference density for loops that cannot be interpreted with reasonable geometry.
Rsym is very similar for data scaled in P3, in all resolution shells. Xtriage does not suggest merohedral twinning.
Nevertheless, I extended my free flags in sftools from P6522 to P32 and cad'd them to amplitudes merged in spacegroup P32. Correspondingly, I expanded my model to a homotetramer and ran Refmac with amplitude based twinning. (Would this be a reasonable input to twin refinement?)
From the output coordinates:
REMARK   3  TWIN DETAILS
REMARK   3   NUMBER OF TWIN DOMAINS  :    4
REMARK   3      TWIN DOMAIN   :    1
REMARK   3      TWIN OPERATOR :  H,  K,  L
REMARK   3      TWIN FRACTION : 0.269
REMARK   3      TWIN DOMAIN   :    2
REMARK   3      TWIN OPERATOR : -K, -H, -L
REMARK   3      TWIN FRACTION : 0.171
REMARK   3      TWIN DOMAIN   :    3
REMARK   3      TWIN OPERATOR :  K,  H, -L
REMARK   3      TWIN FRACTION : 0.258
REMARK   3      TWIN DOMAIN   :    4
REMARK   3      TWIN OPERATOR : -H, -K,  L
REMARK   3      TWIN FRACTION : 0.302
Does this establish twinning versus underestimated symmetry? And what do I need to know about my free-R? Did refmac assign a new flag? Whereas the output file's flags are all 1s and 0s, the input file had 0 ... 19. During the first run, Rfree dropped to <28%. But on a subsequent run, Rfree was stuck >30% when I used the initial job's output MTZ.
Many thanks in advance for your helpful comments.
Wolfram Tempel


Garib N Murshudov 
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road 
Cambridge 
CB2 0QH UK
Email: garib@mrc-lmb.cam.ac.uk 
Web http://www.mrc-lmb.cam.ac.uk