[phenixbb] low resolution map weirdness with newer releases
Scott Classen
sclassen at lbl.gov
Mon Mar 28 16:32:27 PDT 2011
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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