Hi Herman,
Tighter restraints typically close the gap between R and R-free. This does
not mean one should just tighten the restraints to satisfy one's own (or a
referee's) idea of what the gap should be. I don't think there is a clear
target of how large or small the gap should be. If you optimize the
restraints to get the best (free) likelihood, you usually get a reasonable R
gap without explicitly optimizing it.
Cheers,
Robbie
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> Eleanor Dodson
> Sent: Friday, June 21, 2013 14:21
> To: [log in to unmask]
> Subject: Re: [ccp4bb] AW: Twinning problem - almost solved.
>
> At your resolution that seems to me a reasonable gap between R and Rfree?
> Eleanor
>
> On 21 Jun 2013, at 12:28, [log in to unmask] wrote:
>
> > Dear Bulletin Board,
> >
> > After some headbanging (Refmac5 had helpfully created gap records for
all
> insertions and deletions present in the structure), I got refmac5 running
with
> the TWIN option. Refmac5 also found the k,h,-l domain and rejected the
> other possible domains because they were too small. The Rfactor's are now
> extremely good: ~14% and the Rfree's are for me acceptable: ~24%. Since I
> found the difference between R and Rfree somewhat large, I have been
> playing with the weighting. By using a weight of 0.01, I can bring the
Rfactor
> up to 18%, but the Rfree stays about the same or even gets a little worse.
> >
> > My question: is there a way to bring R and Rfree closer together, or is
it
> related to the twinned data and is it something we have to live with?
> >
> > Best regards,
> > Herman
> >
> >
> > -----Ursprüngliche Nachricht-----
> > Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von
> Miller, Mitchell D.
> > Gesendet: Donnerstag, 20. Juni 2013 17:43
> > An: [log in to unmask]
> > Betreff: Re: [ccp4bb] Twinning problem
> >
> > You are welcome. Let me also for the benefit of others who may search
> the archives in the future, let me correct two errors below - (typo and a
miss-
> recollection).
> >
> > Specially, I was thinking that phenix.refine was now able to refine
multiple
> twin laws, but according to Nat Echols on the phenix mailing list
> http://phenix-online.org/pipermail/phenixbb/2013-March/019538.html
> > phenix.refine only handles 1 twin law at this time.
> > (My typo was that and our second structure was 3nuz with twin fractions
> 0.38, 0.32, 0.16 and 0.14 -- not 2nuz).
> >
> > A useful search for deposited structures mentioning tetartohedral
> http://www.ebi.ac.uk/pdbe-
> srv/view/search?search_type=all_text&text=TETARTOHEDRALLY+OR+TETAR
> TOHEDRAL
> >
> > Regards,
> > Mitch
> >
> >
> > -----Original Message-----
> > From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> [log in to unmask]
> > Sent: Thursday, June 20, 2013 8:04 AM
> > To: [log in to unmask]
> > Subject: [ccp4bb] AW: Twinning problem
> >
> > Dear Mitch (and Philip and Phil),
> >
> > It is clear that I should give refmac a go with the non-detwinned F's
and just
> the TWIN command.
> >
> > Thank you for your suggestions,
> > Herman
> >
> >
> >
> > -----Ursprüngliche Nachricht-----
> > Von: Miller, Mitchell D. [mailto:[log in to unmask]]
> > Gesendet: Donnerstag, 20. Juni 2013 16:18
> > An: Schreuder, Herman R&D/DE
> > Betreff: RE: Twinning problem
> >
> > Hi Herman,
> > Have you considered the possibility of your crystals being tetartohedral
> twinned. That is more than one of the twin laws may apply to your
crystals.
> > E.g. in P32 it is possible to have tetartohedral twinning which would
have
> > 4 twin domains - (h,k,l), (k,h,-l), (-h,-k,l) and (-k,-h,-l). Perfect
tetartohedral
> twinning of P3 would merge in P622 and each twin domain would have a
> faction of 0.25.
> >
> > We have had 2 cases like this (the first 2PRX was before there was
support
> for this type of twinning except for in shelxl and we ended up with
refined
> twin fractions of 0.38, 0.28, 0.19, 0.15 for the deposited crystal and a
2nd
> crystal that we did not deposit had twin fractions of 0.25, 0.27, 0.17,
0.31).
> The 2nd case we had was after support for twining (including tetartohedral
> twinning) was added to refmac (and I think phenix.refine can also handle
> this). For 2NUZ, it was P32 with refined twin fractions of 0.25, 0.27,
0.17, 0.31.
> >
> > Pietro Roversi wrote a review of tetartohedral twinning for the CCP4
> proceedings issues of acta D http://dx.doi.org/10.1107/S0907444912006737
> >
> > I would try refinement with refmac using the original (non-detwinned
F's)
> with just the TWIN command to see if it ends up keeping twin fractions for
all
> 3 operators (4 domains) -- especially with crystals 1 and 3 which appear
to
> have the largest estimates of the other twin fractions.
> >
> > Regards,
> > Mitch
> >
> >
> > ==========================================
> > Mitchell Miller, Ph.D.
> > Joint Center for Structural Genomics
> > Stanford Synchrotron Radiation Lightsource
> > 2575 Sand Hill Rd -- SLAC MS 99
> > Menlo Park, CA 94025
> > Phone: 1-650-926-5036
> > FAX: 1-650-926-3292
> >
> >
> > -----Original Message-----
> > From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> [log in to unmask]
> > Sent: Thursday, June 20, 2013 6:47 AM
> > To: [log in to unmask]
> > Subject: [ccp4bb] Twinning problem
> >
> > Dear Bulletin Board,
> >
> > Prodded by pdb annotators, which are very hesitant to accept coordinate
> files when their Rfactor does not correspond with our Rfactor, I had a
look
> again into some old data sets, which I suspect are twinned. Below are the
> results of some twinning tests with the Detwin program (top value: all
> reflections, lower value: reflections > Nsig*obs (whatever that may mean).
> The space group is P32, the resolution is 2.3 - 2.6 Ĺ and data are
reasonable
> complete: 95 - 100%.
> >
> > From the Detwin analysis, it seems that the crystals are twinned with
twin
> operator k,h,-l with a twinning fraction of 0.3 for crystal 1, 0.15 for
crystal 2
> and 0.4 for crystal 3. Crystal 2 can be refined while ignoring twinning to
get
> acceptable but not stellar R and Rfree values. However, when I try to
detwin
> Fobs of e.g. crystal 1 (twinning fraction 0.3), R and Rfree values stay
about
> the same, whatever twinning fraction I try. At the time, I used the CNS
> detwin_perfect protocol to detwin using Fcalcs, which brought the Rfactors
> in acceptable range, but I do not feel that was the perfect solution.
Ignoring
> twinning on e.g. crystal 1 produces an Rfactor of 22% and an Rfree of 29%
> >
> > Do you have any idea what could be going on?
> >
> > Thank you for your help!
> > Herman
> >
> >
> >
> > Crystal 1:
> >
> > operator -h,-k,l
> > Suggests Twinning factor (0.5-H): 0.113
> > Suggests Twinning factor (0.5-H): 0.147
> >
> > operator: k,h,-l
> > Suggests Twinning factor (0.5-H): 0.277
> > Suggests Twinning factor (0.5-H): 0.323
> >
> > operator -k,-h,-l
> > Suggests Twinning factor (0.5-H): 0.101
> > Suggests Twinning factor (0.5-H): 0.134
> >
> >
> > Crystal 2:
> >
> > operator -h,-k,l
> > Suggests Twinning factor (0.5-H): 0.077
> > Suggests Twinning factor (0.5-H): 0.108
> >
> > operator: k,h,-l
> > Suggests Twinning factor (0.5-H): 0.126
> > Suggests Twinning factor (0.5-H): 0.161
> >
> > operator -k,-h,-l
> > Suggests Twinning factor (0.5-H): 0.072
> > Suggests Twinning factor (0.5-H): 0.106
> >
> >
> > Crystal 3:
> >
> > operator -h,-k,l
> > Suggests Twinning factor (0.5-H): 0.123
> > Suggests Twinning factor (0.5-H): 0.149
> >
> > operator: k,h,-l
> > Suggests Twinning factor (0.5-H): 0.393
> > Suggests Twinning factor (0.5-H): 0.433
> >
> > operator -k,-h,-l
> > Suggests Twinning factor (0.5-H): 0.110
> > Suggests Twinning factor (0.5-H): 0.133
> >
> >
> >
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