This is on OSX "Tiger" 10.4.11 on a G5 machine.
Phaser 2.1.1, CCP4 6.0.2
Is anyone else seeing the following ?
In a feature that seems new-ish in Phaser, intermediate solutions get
culled after translation function and before packing tests:
(begin snippet)
Purge solutions according to highest LLG from TFs in other spacegroups
Best Space Group so far: P 61 2 2
Percent used for purge = 0.75
Top LLG value for purge = 28.8034
Mean LLG used for purge = 6.03998
Cutoff LLG used for purge = 23.1125
Number of solutions stored before purge = 33
Number of solutions stored (deleted) after purge = 0 (33)
Purging of the results of the translation function in this spacegroup
using the
highest LLG value so far (from searches in other spacegroups) deleted all
solutions
(end snippet)
which is all well and good, except in this particular case the solutions
for P6122 have LLGs in the 14-16 range.
What Phaser appears to be doing is picking up the best case LLGs (and
therefore LLG cutoffs) for translation function peaks from another space
group (P622), none of which passed the packing criteria, and then
inappropriately applying them to subsequent trial solutions in
subsequent space groups that have lower LLGs may in fact be better
candidate solutions and survive the packing test.
In the normal course of events, you'd hope that the best LLG corresponds
to the correct solution in the correct space group, but I'll gladly
concede that I'm using a marginal model with unimpressive data, and
it'll probably fail anyway. This feature in Phaser would seem to
potentially speed up correct solutions with good models and data when
using SGALTERNATIVE ALL but may in fact make the performance worse with
bad models and poor data.
Unless I've missed something here, the LLG score/cutoff test needs to be
based on trial solutions that have survived the packing test, not peaks
from the translation function before that test.
I'm using a fairly conventional script (not the GUI) in this case.
#
phaser << EOF
MODE MR_AUTO
HKLIN ptcr1680_pk_truncate.mtz
LABIN F=F SIGF=SIGF
TITLE Just a phaser script
COMPOSITION PROTEIN MW 28000 NUMBER 3
RESOLUTION 10. 3.2
SGALTERNATIVE ALL
ENSEMBLE ensemble1 PDBFILE helix_16.pdb IDENT 75.0
SEARCH ENSEMBLE ensemble1 NUMBER 1
ROOT phaser1
END
EOF
