Is this twinning or several crystals indexed according to different
conventions? You usually see evidence of twinning for each crystal if it is
really there..
Trigonal data can be indexed as h,k,l k,h,-k -h,-k,l or -k,-h,-l of course
so you have a 75% chance of getting the 2nd crystal on a different
convention than the first.. POINTLESS checks for this if you give it pairs
of input files and does a good job in selecting the same indexing
convention - providing of course the twinning isnt present.
I would be suspicious because
a) I have been convinced by having more than 2 twin domains b) when there
is twinning the data analysis on each crystal seperately shows it up.
Eleanor
- On Mar 2 2012, 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
--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266
