I agree that looking at the packing is a good idea, but I also agree that having the wrong space group is a likely possible explanation. That’s the most common scenario when there are many clashing solutions with high TFZ scores.
Randy Read On 17 Jun 2014, at 15:52, Roger Rowlett <[email protected]> wrote: > Increase the number of allowed clashes in Phaser, re-run it then look at the > packing of the solution found and identify the source of the clashes. > Possibilities for the clash issue include: > Wrong space group > Flexible loops or termini in search model not present or differently > arranged in your crystal target > Once you look at the packing in Coot or Pymol, you will have a good idea of > what to do next. If the problem is flexible loops or misplaced N- or > C-termini, you can delete these regions from your search model (they are not > helping you phase anyway) and re-run Phaser with an appropriately truncated > search model. > Cheers, > > _______________________________________ > Roger S. Rowlett > Gordon & Dorothy Kline Professor > Department of Chemistry > Colgate University > 13 Oak Drive > Hamilton, NY 13346 > > tel: (315)-228-7245 > ofc: (315)-228-7395 > fax: (315)-228-7935 > email: [email protected] > > On 6/17/2014 10:44 AM, Almudena Ponce Salvatierra wrote: >> Dear ccp4 users, >> >> I get the following message from Phaser when I do a molecular replacement >> with two ensembles. One of the ensembles is placed but the second one is not >> placed, and then it says this: >> >> Solutions with Z-scores greater than 13.0 (the threshold indicating a >> definite >> solution) were rejected for failing packing test >> #1 TFZ=16.8 PAK=487 >> #2 TFZ=17.4 PAK=440 >> #3 TFZ=17.0 PAK=312 >> #4 TFZ=16.7 PAK=294 >> #5 TFZ=16.8 PAK=227 >> #6 TFZ=16.6 PAK=284 >> #7 TFZ=16.2 PAK=219 >> #8 TFZ=16.3 PAK=287 >> #9 TFZ=16.1 PAK=186 >> #10 TFZ=16.6 PAK=277 >> #11 TFZ=16.7 PAK=204 >> #12 TFZ=16.8 PAK=404 >> #13 TFZ=15.9 PAK=271 >> #14 TFZ=15.8 PAK=194 >> #15 TFZ=14.9 PAK=229 >> #16 TFZ=16.4 PAK=368 >> #17 TFZ=17.3 PAK=194 >> #18 TFZ=15.2 PAK=240 >> #19 TFZ=16.1 PAK=325 >> #20 TFZ=15.3 PAK=455 >> #21 TFZ=16.5 PAK=298 >> #22 TFZ=16.6 PAK=290 >> #23 TFZ=15.2 PAK=259 >> #24 TFZ=16.2 PAK=194 >> #25 TFZ=16.1 PAK=314 >> #26 TFZ=16.3 PAK=194 >> #27 TFZ=16.3 PAK=387 >> #28 TFZ=15.6 PAK=193 >> #29 TFZ=15.7 PAK=219 >> #30 TFZ=15.6 PAK=474 >> #31 TFZ=15.1 PAK=194 >> #32 TFZ=15.4 PAK=339 >> #33 TFZ=15.5 PAK=210 >> #34 TFZ=15.2 PAK=300 >> #35 TFZ=15.6 PAK=186 >> #36 TFZ=16.2 PAK=216 >> #37 TFZ=14.9 PAK=182 >> #38 TFZ=15.7 PAK=279 >> #39 TFZ=15.5 PAK=285 >> #40 TFZ=15.0 PAK=374 >> #41 TFZ=15.4 PAK=404 >> #42 TFZ=15.3 PAK=185 >> #43 TFZ=15.6 PAK=227 >> #44 TFZ=14.8 PAK=364 >> #45 TFZ=15.7 PAK=193 >> #46 TFZ=14.5 PAK=448 >> #47 TFZ=14.6 PAK=219 >> #48 TFZ=15.5 PAK=210 >> #49 TFZ=15.7 PAK=189 >> #50 TFZ=15.0 PAK=193 >> #51 TFZ=15.0 PAK=281 >> #52 TFZ=15.2 PAK=202 >> >> And the list still continues for a bit. How should I think about this? I >> would assume that the clashes are too many only by seeing those numbers, but >> maybe there is something else to take into account? >> >> Thanks a lot in advance. >> >> Best wishes, >> >> Almudena >> >> >> -- >> Almudena Ponce-Salvatierra >> Macromolecular crystallography and Nucleic acid chemistry >> Max Planck Institute for Biophysical Chemistry >> Am Fassberg 11 37077 Göttingen >> Germany >> > ------ 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: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
