[phenixbb] simulated annealing

jp d yoyoq at yahoo.com
Fri Jun 18 17:05:04 PDT 2010

i  am having trouble with simulated annealing and have finally got it 
down to a test case that only takes 10 minutes to fail.
using supplied phenix examples  1rxf.mtz  and  1rxf_randomise.pdb 
i can run the following command and it fails 
in phenix1.6.2  but not in phenix1.5-2

the error is:  
RuntimeError: Bond distance > max_reasonable_bond_distance: 52.1931 > 50

command line arguments:

phenix.refine 1rxf.mtz  \
          1rxf_randomise.pdb wxc_scale=0.5 \
           write_geo_file=False xray_data.low_resolution=60 \
           disulfide_distance_cutoff=2.4 \
           discard_psi_phi=False \
           xray_data.high_resolution=5 \
           strategy=individual_sites \
           interleaved_minimization.number_of_iterations=2 \
           main.simulated_annealing=true \
           simulated_annealing.start_temperature=550000 \
           simulated_annealing.cool_rate=450000 \
           --overwrite \
           --show-process-info \
           > junk_cast2.log

should i stick with 1.5 for simulated annealing?

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