Yes, the current version of Phaser will do the same test that xtriage carries out, and if it finds a sufficiently high non-origin Patterson peak, it will automatically characterise the translational NCS and use this for molecular replacement. This is working pretty well in our tests.
In the near future you will be able to get the current version of Phaser as part of the upcoming CCP4 release, but at the moment the easiest way to get it is to download a recent version of Phenix. You should be able to run that through ccp4i by downloading and installing the updated GUI files from our website (and getting ccp4i to interpret the command "phaser" as "phenix.phaser"). Best wishes, Randy Read On 12 Mar 2012, at 16:06, Anastassis Perrakis wrote: > Hi - > > I agree with Garib that its likely a pseudo-translation issue. > I also agree with that the advice he gives is correct, but ... > ... since I am evidently less smart to follow all these steps, > I like to use phenix.xtriage that will tell me if there is > pseudo-translation or not, > and will give a p-value for that being significant. Its at the end of the > text output. > > I am not sure if Phaser deals these days with pseudo-translation - I guess > Randy can tell us. > If not, there is a very simple trick to make Phaser work with > pseudo-translation, > but since I threw the ball to Randy's court and he told me the trick a few > years ago, > I will let him explain only if needed ;-) > > Best, > > Tassos > > On Mar 11, 2012, at 12:55, Garib N Murshudov wrote: > >> 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 >> >> >> > > P please don't print this e-mail unless you really need to > Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member > Department of Biochemistry (B8) > Netherlands Cancer Institute, > Dept. B8, 1066 CX Amsterdam, The Netherlands > Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791 > > > > ------ 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
