[phenixbb] Help making selections
James Fraser
jamesfraser at berkeley.edu
Thu Aug 23 14:04:23 PDT 2007
I am trying to refine a structure where I want chains C and D refined
anisotropically. Chain A refined isotropically and as a TLS group.
Chain B refined isotropically and as a (separate) TLS group. Chain S
(waters) just refined isotropically.
I've tried playing around with selections on the command line and in
the .def file. Yet always end up not getting the refinement to run
correctly or have phenix.refine throw an "AssertionError". I'm using
the latest CCIapps phenix.refine. Can someone help me out. Below are
the excerpt from the DEF file and the error message thrown to the
screen.
Thanks,
James
--FROM DEF FILE--
refine {
strategy = *individual_sites rigid_body *individual_adp group_adp *tls \
individual_occupancies group_occupancies group_anomalous none
sites {
individual = None
rigid_body = None
}
adp {
individual {
isotropic = None
anisotropic = "chain c or chain d"
}
group = None
one_adp_group_per_residue = True
tls = "chain a"
tls = "chain b"
}
occupancies {
individual = None
group = None
one_occupancy_group_per_residue = False
}
anomalous_s
--FROM LOG FILE--
----------Target weights (before refinement)----------
Traceback (most recent call last):
File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/phenix/phenix/command_line/refine.py",
line 5, in ?
command_line.run(command_name="phenix.refine", args=sys.argv[1:])
File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/phenix/phenix/refinement/command_line.py",
line 80, in run
refine_object.run(
File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/phenix/phenix/refinement/driver.py",
line 1244, in run
log = log)
File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/phenix/phenix/refinement/strategies.py",
line 268, in refinement_machine
log = log)
File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/phenix/phenix/refinement/weight_xray_chem.py",
line 137, in __init__
compute_gradients = True)
File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/mmtbx/mmtbx/restraints.py",
line 126, in energies_adp_aniso
xray_structure = xray_structure,
File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py",
line 113, in __init__
self.check_flags(fl_i)
File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py",
line 181, in check_flags
assert not fl.use_u_aniso()
AssertionError
--
James Fraser
jamesfraser at berkeley.edu
Alber Lab
356 Stanley Hall, QB3
UC Berkeley
Berkeley, CA 94720
http://ucxray.berkeley.edu/~jfraser/
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