Are your unit cell and SG correct? I think you maybe should reindex to get a cell volume 25% of this one, and maybe SG P21 That patterson peak is enormous.. Eleanor On 1 Aug 2012, at 08:45, Qixu Cai wrote:
> Dear Randy, > > Thanks very much for your detailed explanation and helpful advice. I have run > the phaser job just as you have said. This is the result. > > The resolution of this dataset is 2.45A. > > ===================================================================== > > I added the three commands to phaser job for all alternative space group of > P212121: > > TNCS USE ON > TNCS NMOL 4 > TNCS PATT PERCENT 80.0 > > The phaser got a SINGLE solution for space group P22121, and Rval=88.2 > > SOLU SET RFZ=14.5 TFZ=22.3 PAK=0 +TNCS PAK=0 +TNCS PAK=0 +TNCS PAK=0 > LLG=2565LLG=4322 > SOLU SPAC P 2 21 21 > SOLU 6DIM ENSE ensemble1 EULER 91.7 89.4 90.3 FRAC 0.49 0.51 0.99 BFAC 0.00 > SOLU 6DIM ENSE ensemble1 EULER 269.3 89.4 90.2 FRAC -0.01 -0.00 0.74 BFAC > 0.00 > SOLU 6DIM ENSE ensemble1 EULER 269.0 89.1 90.0 FRAC 0.49 -0.00 1.00 BFAC > 0.00 > SOLU 6DIM ENSE ensemble1 EULER 91.5 89.3 90.2 FRAC 0.99 0.51 0.74 BFAC 0.00 > > After 50 cycles rigidbody refinement, R/Rfree=0.36/0.37 > After 50 cycles restraint refinement (with jellybody refine and twin refine), > R/Rfree=0.31/0.35 > After several cycles of coot model building and restraint refinement, > R/Rfree=0.27/0.31 > After finding waters, R/Rfree=0.2478/0.2984 > > =================================================================== > If I run phaser job without those three added commands, the phaser got single > solution at P21212 space group (Rval=0.3%): > > > SOLU SET RFZ=17.0 TFZ=20.1 PAK=0 LLG=457 TFZ==16.2 RFZ=16.3 TFZ=62.1 PAK=0 > LLG=2599 TFZ==19.8 (& TFZ=59.0 PAK=0 LLG=2403) LLG+=(2608 & 4349) LLG=4200 > TFZ==22.2 PAK=0 RFZ=10.8 TFZ=56.4 PAK=0 LLG=5751 TFZ==22.5 LLG=9274 > TFZ==27.5 > SOLU SPAC P 21 21 2 > SOLU 6DIM ENSE ensemble1 EULER 90.0 90.7 270.1 FRAC -0.00 0.26 0.13 BFAC > -4.09 > SOLU 6DIM ENSE ensemble1 EULER 271.2 89.4 90.3 FRAC 0.01 0.24 -0.38 BFAC > -3.00 > SOLU 6DIM ENSE ensemble1 EULER 270.3 90.8 270.1 FRAC 0.50 -0.25 -0.12 BFAC > -1.25 > SOLU 6DIM ENSE ensemble1 EULER 87.5 90.6 270.4 FRAC 0.02 0.26 -0.37 BFAC > 11.58 > > And the electron density is worse than the P22121 solution. > > ====================================================================== > Just as I have said last email, I can also get single solution at P212121 > space group, > > and after 50 cycles rigidbody refinement and 50 cycles restraint refinement > with jellybody and twin, I can get R/Rfree=0.30/0.33. > > But the electron density is worse than the P22121 solution, so I do not carry > out the model building in coot. > > ======================================================================= > > My questiones: > > 1) Is the P22121 solution is my correct solution? These three solutions > really confused me. > > 2) Why the R/Rfree is high even after I have good electron density and have > found waters? (R/Rfree=0.478/0.2984 for 2.45A data) > > 3) What's the function of the command "TNCS USE ON"? Is it necessary? > > 4) I found if I used twin refinement in refmac5, the R/Rfree would decrease > about 0.02 comparing to without twinn refinement. Is it reasonable? Is there > any tNCS refinement options in refmac? > > Thanks for your help. > > Best wishes, > > Qixu Cai > > > > > 2012/7/31 Randy Read <rj...@cam.ac.uk> > Hi, > > The second Patterson peak is twice the first (considering lattice > translations, where 1 is equivalent to 0 modulo 1), and then if you triple > the first vector you'll get minus the first vector (again considering lattice > translations, i.e. 3/4 is equal to 1 - 1/4 which is equivalent to > -1/4), which is equivalent by symmetry to the first vector so wouldn't appear > in the peak list. So the Patterson indicates 4 copies separated by 0, 1, 2 > and 3 times the top Patterson vector, in approximately the same orientation. > > We've haven't fully dealt with the complications of multiple tNCS-related > copies in Phaser yet, but for this type of case there is a reasonable > treatment. You should add two commands to the Phaser job: > > TNCS NMOL 4 > TNCS PATT PERCENT 80 > > The first says that the Patterson translation is repeated 4 times, and the > second will cause the second Patterson peak to be ignored. > > I'd suggest repeating the Phaser run with these commands and making sure that > you end up with the same solution as you got when the tNCS was ignored. When > tNCS is ignored, it's possible to end up with a solution that is only > partially correct, which would be one explanation for having some molecules > that look better in density than others. > > Best wishes, > > Randy Read > > On 31 Jul 2012, at 13:11, Qixu Cai wrote: > > > It's a P212121 dataset. I have used phaser to find four solution in ASU. > > > > This is the phaser log file: > > ------------------------------------------------------------ > > PEUDO-TRANSLATIONAL NCS VECTOR > > -------------------------------------------------------------- > > > > Space Group : P 21 21 21 > > Patterson Symmetry: P m m m > > Resolution of All Data (Number): 2.45 49.00 (22968) > > Resolution of Patterson (Number): 5.00 9.99 (2364) > > There were 2 non-origin distinct peaks (i.e. more than 15 angstroms from > > the > > origin) > > > > <!--SUMMARY_BEGIN--> > > 84.1% origin: FRAC 0.500 0.000 0.250 (ORTH 32.0 0.0 32.2) > > 72.2% origin: FRAC 0.000 0.000 0.500 (ORTH 0.0 0.0 64.4) > > <!--SUMMARY_END--> > > > > More than one pseudo-translational ncs vector found > > Correction factors will not be applied > > > > > > PS: I have used phenix.xtrige and found the p-value of > > pseudo-translational ncs is very little, which indicates the exist of > > the pseudo-translational ncs. And no twin found in this dataset. > > > > Now the problem is two in the four molecules of an ASU have worse > > electron density than the other two molecules. And after rigidbody and > > restraint refinement by refmac without "twin refinement", the R/Rfree > > is a little high (0.33/0.36). And if I turn on the "twin refinement" > > in refmac, the R/Rfree is 0.30/0.33. > > > > So, my question is, there is not twin in my data but > > pseudo-translational ncs, is it suitable to use "twin refinement" in > > refmac, which has a good R/Rfree result. > > > > Thanks a lot for your help. > > > > Best wishes, > > > > Qixu Cai > > > > > > 2012/7/31, Eleanor Dodson <eleanor.dod...@york.ac.uk>: > >> More details - what do you mean by pesudo-translational symmetry ? > >> Are there two molecules related by a translation vector? or its it > >> something more complicated? > >> Eleanor > >> > >> On 31 July 2012 10:47, Qixu Cai <caiq...@gmail.com> wrote: > >> > >>> Dear all, > >>> > >>> Can I use the "twin refinement" to refine the pesudo-translational > >>> symmetry dataset? > >>> > >>> Thanks a lot for your help. > >>> > >>> Best wishes, > >>> > >>> Qixu Cai > >>> > >> > > > > > > -- > > Qixu Cai > > Email: caiq...@gmail.com > > School of Life Sciences, > > Xiamen University, Fujian, China > > ------ > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: + 44 1223 336500 > Wellcome Trust/MRC Building Fax: + 44 1223 336827 > Hills Road E-mail: rj...@cam.ac.uk > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > >
