Hi Could you please check: 1) If there is psedotranslation. It could be done by using sfcheck, molrep, ctruncate or calculating patterson map and displaying using coot at 8-10 sigma level (it is my favourite method for analysis of pseudo translations), whole unit cell ( a bit bigger than whole unit cell). Then if you see large no origin peak (very likely along one of the axis, could be a). If yes then you have several options: using phaser - 1) reduce cell, find solution in smaller cell and then expand; 2) use molrep to solve. When there are two copies related with pseudo translation molrep can give you solution; 3) as far as I am aware latest version of phaser works with pseudo translation. If you have pseudtranslation you should be aware that even if you solve the structure starting R factors could be 70-80%. Then you may want to do 40 cycles of rigid body and 40-100 cycles of ljelly body 2) Check your space group in pdb and mtz file. They may not be consistent.
I hope it helps. Garib On 11 Mar 2012, at 07:33, xiaoyazi2008 wrote: > Hi All, > > I have an interesting thing to share. > 2.3A dataset with good quality, P21 > Partial model is available (~60% of the target protein). > It seems that there are 4 copies in the ASU (Matthews_coef 2.6, 53%solvent) > Molecular replacement gave two copies of the model (Z scores are R6.2, T6.2, > R6.8, T13.4). The solution is very clear. It could not locate the rest two > copies. > > However, a quick refmac5 refinement gave a very high R factor. > The funny part is the symmetry operation in Coot. > As shown in the JPEG figure, it looks like there should be another two copies > (based on strong fo-fc green map), which locate in the empty space between > models found by Phaser. > > Why is that Phaser could not find the remaining two copies even there are > strong fo-fc density? > Any suggestions... > > > Thanks a lot! > > Zhihong > <weird thing.jpg> Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
