[phenixbb] den refinement

Andreas Förster docandreas at gmail.com
Tue Jun 11 08:44:45 PDT 2013


Dear all,

I'm trying to get DEN refinement going from the command line.  The run 
aborts quickly with the following error in the log file:

Sorry: Cartesian simulated annealing should not be turned on for DEN 
refinement. Annealing settings are controlled in the den parameter scope.

The DEN scope in input.def looks like this:

   den {
     reference_file = den_ref_Jun.pdb
     gamma = 0.5
     kappa = 0.1
     weight = 30
     sigma = 0.44
     optimize = True
     opt_gamma_values = 0 0.2 0.4 0.6 0.8 1
     opt_weight_values = 3 10 30 100 300
     num_cycles = 12
     kappa_burn_in_cycles = 2
     bulk_solvent_and_scale = True
     refine_adp = True
     final_refinement_cycle = False
     verbose = False
     annealing_type = *torsion cartesian
     output_kinemage = False
     restraint_network {
       lower_distance_cutoff = 3
       upper_distance_cutoff = 15
       sequence_separation_low = 0
       sequence_separation_limit = 10
       exclude_hydrogens = True
       ndistance_ratio = 1
       export_den_pairs = False
       den_network_file = None
     }

Annealing type is torsion from what I can tell.  What am I doing wrong?

(Release tag: 1394, Platform: intel-linux-2.6-x86_64 redhat-e6.2)


Thanks.


Andreas


-- 
         Andreas Förster, Research Associate
         Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
             http://www.msf.bio.ic.ac.uk


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