Dear Tim, I normally do not use Refmac, so I have no idea what to expect and what would be a good weight. I will do the molprobity test, but I do not expect major problems. This is a MR structure with a high resolution search model with 100% sequence identity. A few amino acids may have problems, but the overall structure should be ok. E.g. Refmac lists an RMSD bonds of 0.008 Å and an RMDS bond angles of 1.3°. Anyway, if the structure turns out to be really bad, I will get punished by the PDB annotators with lots of REMARK 500 records!
Best, Herman -----Ursprüngliche Nachricht----- Von: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Gesendet: Freitag, 21. Juni 2013 17:30 An: Schreuder, Herman R&D/DE Cc: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: Twinning problem - almost solved. -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Herman, a large gap between R and Rfree might indicate a horrible geometry of your structure, especially if R increased by lowering the matrix weight in refmac. Or, to put it the other way round: it is easy to achieve a low R-value by screwing up the geometry of your model. Did you run the PDB file through molprobity? My guess is with the R=14% model you get a very red chart... Best, Tim On 06/21/2013 04:45 PM, herman.schreu...@sanofi.com wrote: > Hi Robbie, > > That is what I tried. The Rfactor got a lot worse (14%->18%) and the > Rfree got a little worse (by 0.1-0.2%). My feeling is that that is not > the right approach. Roger Rowlett suggested to give PDB_REDO a try. > Maybe you have some instructions available how to get a local version? > > Best, Herman > > -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board > [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Robbie Joosten > Gesendet: Freitag, 21. Juni 2013 16:21 An: CCP4BB@JISCMAIL.AC.UK > Betreff: Re: [ccp4bb] AW: Twinning problem - almost solved. > > 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor Dodson Sent: >> Friday, June 21, 2013 14:21 To: CCP4BB@JISCMAIL.AC.UK 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, 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+TETAR >> >> TOHEDRAL >>> >>> 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 >>> >>> >>> > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRxHGKUxlJ7aRr7hoRAoOPAKDa7eOFTpFL23wy+VYjuhy+iFo7OQCdG6Ka Uuj6RQAk7xv0WtZO99i6ZYE= =Niti -----END PGP SIGNATURE-----
