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 rrowl...@colgate.edu 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: rrowl...@colgate.edu
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 RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
