Re: [phenixbb] low resolution map weirdness with newer releases

28 Mar 2011

      Hi Scott,

can you send me the inputs off-list so I can reproduce this myself... So 
far I have no idea why this is happening.

Pavel.

On 3/28/11 4:32 PM, Scott Classen wrote:
...
Something changed between  build 432 and 486 that made my low resolution maps look much crappier. See attached tiff. See if you can guess which map was produced by the release 486.
def file looks more or less like this (from a --diff-params):
refinement {
  crystal_symmetry {
    unit_cell = top secret
    space_group = top secret
  }
  input {
    pdb {
      file_name = "../4_23_003.pdb"
    }
    xray_data {
      file_name = "../4_23.sca.mtz"
      labels = "4_23.sca,SIG4_23.sca"
      high_resolution = 3.9
      r_free_flags {
        file_name = "../4_23.sca.mtz"
        label = "R-free-flags"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "test-486"
    serial = 1
  }
  refine {
    strategy = *individual_sites individual_sites_real_space rigid_body \
               individual_adp group_adp tls occupancies group_anomalous
    sites {
      individual = "chain A and resseq 100:107"
      individual = "chain B and resseq 500:507"
      individual = "chain E and resseq 100:107"
      individual = "chain F and resseq 500:507"
      individual = "chain C and resseq 111:117"
      individual = "chain D and resseq 111:117"
      individual = "chain G and resseq 111:117"
      individual = "chain H and resseq 111:117"
      individual = "chain C and resseq 63:68"
      individual = "chain D and resseq 63:68"
      individual = "chain G and resseq 63:68"
      individual = "chain H and resseq 63:68"
      rigid_body = "chain A"
      rigid_body = "chain B"
      rigid_body = "chain C"
      rigid_body = "chain D"
      rigid_body = "chain E"
      rigid_body = "chain F"
      rigid_body = "chain G"
      rigid_body = "chain H"
    }
  }
  main {
    number_of_macro_cycles = 1
    secondary_structure_restraints = True
    random_seed = 3141766
    optimize_mask = False
  }
  modify_start_model {
    adp {
      set_b_iso = 50
    }
  }
  fake_f_obs {
    mask {
      ignore_hydrogens = True
    }
  }
  geometry_restraints.edits {
    excessive_bond_distance_limit = 20
  }
  mask {
    ignore_hydrogens = True
  }
  simulated_annealing {
    start_temperature = 300
    final_temperature = 200
  }
  target_weights {
    wxc_scale = 0.4
  }
  ias {
    b_iso_max = 60
  }
  secondary_structure {
    h_bond_restraints {
      substitute_n_for_h = True
      remove_outliers = False
      sigma = 0.02
      h_o_distance_ideal = 2.95
      h_o_distance_max = 5
      n_o_distance_ideal = 2.95
      n_o_distance_max = 5
    }
}
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Re: [phenixbb] low resolution map weirdness with newer releases

Pavel Afonine