[phenixbb] low resolution map weirdness with newer releases

Paul Adams pdadams at lbl.gov
Mon Mar 28 16:46:03 PDT 2011


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 <sclassen at lbl.gov> 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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