I have found PDB_REDO is an efficient way of tweaking structure solutions. Among other things, it sorts through various MATRIX and BFAC weights and tests effectiveness of TLS if not used already. It usually improves typical "final" structure solutions for our group by about 1% or so Rfree and reduces the Rfree-R spread, as well as improves a variety of other structural measures.
You can of course adjust weights and TLS manually, but if you can get a local version of PDB_REDO running it saves a lot of time, and has some extra features. I've modified v. 5.0.9 for this purpose. Depending on the packages you do or don't have, it is a little tricky to get running locally. Roger Rowlett On Jun 21, 2013 4:42 AM, <herman.schreu...@sanofi.com> 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:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von > Miller, Mitchell D. > Gesendet: Donnerstag, 20. Juni 2013 17:43 > An: CCP4BB@JISCMAIL.AC.UK > 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+TETARTOHEDRAL > > Regards, > Mitch > > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > herman.schreu...@sanofi.com > Sent: Thursday, June 20, 2013 8:04 AM > To: CCP4BB@JISCMAIL.AC.UK > 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:mmil...@slac.stanford.edu] > 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > herman.schreu...@sanofi.com > Sent: Thursday, June 20, 2013 6:47 AM > To: CCP4BB@JISCMAIL.AC.UK > 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 Å 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 > > > >
