Hi Andreas,
My guess is that you have main.simulated_annealing=True also active in your
parameter file. You need to set this to False, and then the refinement
should proceed.
Jeff
On Tue, Jun 11, 2013 at 11:44 AM, Andreas Förster
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 ______________________________**_________________ phenixbb mailing list [email protected] http://phenix-online.org/**mailman/listinfo/phenixbbhttp://phenix-online.org/mailman/listinfo/phenixbb