Dear Jürgen, Although not a phaser developer, here are some comments from my side:
Try to collect data on a many crystals as you can lay your hands on and don't look at resolution alone. A 3.0 Å solvable data set is much more useful than a 1.7 Å unsolvable one. Also once you have figured out the crystal packing in a low-resolution crystal, you can use that information to solve the high resolution structure. I guess you have looked at all the usual twinning tests and indicators. However, just ignoring twinning can produce very reasonable-looking electron density maps. The phases from the untwinned model together with the matching twin contribution in your data will produce nice electron density, while the same phases with the "wrong" twin contribution will produce mainly noise. This could explain your sort of right electron density maps with very bad Rfactors. In fact, the PDB seems to contain quite a number of older structures with undetected twinning. In my hands, phaser starts burning CPU time when there are no clear intermediate solutions and phaser has to test a huge number of possible solutions and combinations of solutions. However, here the phaser developers are the people to help you. Good luck! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Jurgen Bosch Gesendet: Mittwoch, 1. Oktober 2014 04:03 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Phaser question, twinning, DIALS, suggestions welcome Dear BB, or in particular Phaser developers :-) This must be part of British humor right (or was that the Canadian influence Randy) ? eLLG indicates that placement of ensemble "ensemble_1" will be straightforward The data are sufficient to exceed the eLLG target The search space is finite 143 x 143 x 80 Å with 3 or 4 molecules per asu, but Phaser has been burning CPU cycles quite a bit, we are approaching 24h by now. Data extends to 1.7 Å - for MR we cut at 2.5 Å. I can hear Garib, yes, Molrep was done in few minutes but I'm not super convinced about the solution either. Same with BALBES and MrBump (which took a few more minutes, actually also days for MrBump) The space group appears to be P63 22 as judged by XDS, pointless, xtriage, however the crystals are split (at least in some areas it's visible) but I thought XDS would take care of these "aliens" and eliminate them mostly. My graduate student, Lauren, found a nifty program called DIALS that we wish to explore further to rescue the "nice" data we have and hopefully solve the structure. Lower symmetry space groups were tried down to P21 with increasing number of molecules per asu and applying twin laws if necessary. The minor problem with the twins is how do I really know that it is a higher symmetry space group and not a 50% twin in a lower symmetry ? Rwork/Rfree in this particular case do not seem to help at all for distinguishing between the solutions. Maps looks sort of right but R-factors are not reflecting what you see on the screen. We appreciate any suggestions and ideas what else we could do. Thanks, Jürgen ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742<tel:%2B1-410-614-4742> Lab: +1-410-614-4894<tel:%2B1-410-614-4894> Fax: +1-410-955-2926<tel:%2B1-410-955-2926> http://lupo.jhsph.edu
