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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