Help making selections

23 Aug 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
[email protected]
Alber Lab
356 Stanley Hall, QB3
UC Berkeley
Berkeley, CA 94720
http://ucxray.berkeley.edu/~jfraser/

James Fraser

Pavel Afonine

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