Re: [phenixbb] phaser spacegroup within phenix
Hi Nat
I don't think its a bug, just phaser getting a little bit confused. Phaser ran in both P2 and P21 using the phenix default, not P21 - the space group of the mtz. This default is probably the right thing to do if you don't know the space group of your crystal, but then you wouldn't have scaled the mtz in P21.
In my case the reason phaser failed to find a solution is that the P2 solution had a higher initial LLG than the P21 solution while finding the first copy of 4 in my A.U.. So phaser picked P2 to continue the molecular replacement and subsequently stopped due to clashes during packing.
John
On Tue, Jun 15, 2010 at 8:45 AM, John M. Berrisford
I have an mtz processed in P21 and when I load it into the phenix phaser GUI it tells me its P21 (P 1 21 1) and gives me no other options. However, when I run the molecular replacement job it decides that the space group could be either P2 or P21 and runs both - which in my case runs in P2 and gives a partial solution, not the full solution I would expect in P21. A bit annoying as I know my space group is actually P21. After a few minutes of head scratching, the only way I found to fix it to run in P21 is to enter the "other settings" menu and select "none" within "alternative space groups". I guess this is what your suppose to do, but its not obvious.
Point taken - I'll move this to the main window (and label it more clearly - sorry). The result you're describing sounds like it might be a bug, though; shouldn't Phaser try P21 as well and get the full solution, instead of settling for P2? This is what I would expect for the default behavior. -Nat -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44 1223 252882
the P2 solution had a higher initial LLG than the P21 solution while finding the first copy of 4 in my A.U.. So phaser picked P2 to continue the molecular replacement and subsequently stopped due to clashes during packing.
I wonder how often this happens. And it worries me.. use_all_plausible_sg = False is the default in the command line version of phenix automr... was it enabled by default for the gui? F --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
On Wed, Jun 16, 2010 at 5:01 AM, Francis E Reyes wrote: use_all_plausible_sg = False is the default in the command line version of
phenix automr... was it enabled by default for the gui? For AutoMR, no (the GUI rarely modifies the default behavior of programs).
After looking at the AutoMr code, I'm still not exactly sure what this
option does, but I assume it's equivalent to either searching "all" or
"hand" (which I think means the space group and its enantiomorph).
For Phaser, the default is now "hand", for both the command-line version and
the GUI. CCP4 is using an older version of Phaser, which I believe only
used the assigned space group and didn't try anything else.
-Nat
participants (3)
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Francis E Reyes -
John M. Berrisford -
Nathaniel Echols