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

1 Apr 2011

      Hi Scott,

this problem should be solved starting PHENIX nightly build version 
dev-717 and up.

The maps should be similar to what you had using 432 or better, please 
let me know otherwise.

Pavel.

On 3/28/11 5:14 PM, Scott Classen wrote:
...
Hi Paul,
Yes I tried the nightly build (712), and the maps remain flat and featureless. Pavel is looking into it.
If anything useful comes of it I/we will post on the Phenix list for everyones benefit.
Cheers,
Scott
On Mar 28, 2011, at 4:46 PM, Paul Adams wrote:
...
You might want to try a recent developer build as well.
Paul Adams
Sent from my iPhone
On Mar 28, 2011, at 7:32 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
  }
}
<432-vs-486-lores.png>
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Re: [phenixbb] low resolution map weirdness with newer releases

Pavel Afonine