Can someone point me to bulletpoint documentation on using the twin
refinement in CCP4?
Here's what I did.
1. I'm in space group P3, and the see a very clean diffraction pattern
that looks like one single lattice. Very clean spots, so merohedral
twinning.
2. You can use various programs to estimate the twin fraction and select
various twin laws.
3. You run DETWIN in the UTILITIES section of DATA REDUCTION and
ANALYSIS. I have both intensities IMEAN and amplitudes FMEAN, and selected
amplitudes. The FMEAN changes to something like FMEAN_detw. You have to
select a twin fraction, but does it matter what the twin factor you assign
is? (It seems to get refined, or just estimated, in refinement?)
4. There are potentially 3 twin laws, so do you run DETWIN three times?
You can, in fact, get amplitudes that are FMEAN_detw_detw_detw. I've run
it once and three times, and seems to give the same result in REFMAC
refinement.
5. Select the Free R subset. Will uniqueify choose correctly?
6. In REFMAC, it looks for the F_detw amplitude, or you can select it.
Then it seems to select and test three twin laws, even if you only ran
DETWIN once, with one selected twin law. It tests if the twin laws give
low R(merge). If not, it tosses them out. It seems like the R(merge)
calculation depends on the starting model, and not just on the modified
Fobs data. It also seems like it tries to calculate the twin fraction, and
then refine the structure. Or, is it just giving an estimate, and I need
to go back to original data and rerun DETWIN?
7. I tried to work with intensities instead of amplitudes, and it can
blow up. I've also refined, got a good refinement (3 twin laws, each with
twin fraction around 0.1, Rcryst = 19%, Rfree = 21%), rebuilt one chain of
the structure, and it blows up, suggesting no twinning, but Rs around 35%.
Does REFMAC refine the twin fraction?
Do I have to assign a twin fraction in DETWIN, or does it just set up the
relationships between reflections and amplitudes?
Should I try to work with intensities or amplitudes. The calculation is
presumably done on intensities, but seems to be more unstable using that
option.
I haven't tried the PHENIX option. Just a quick step-by-step guide on what
to do would be useful.
Thanks,
Bernie
--
Bernard D. Santarsiero
Research Professor
Center for Structural Biology
University of Illinois at Chicago
MC870 3070MBRB 900 South Ashland Avenue
Chicago, IL 60607-7173 USA
(312) 413-0339 (office)
(312) 413-9303 (FAX)
http://www.uic.edu/labs/bds
http://scholar.google.com/citations?user=fGauLBMAAAAJ
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