[phenixbb] low resolution map weirdness with newer releases

Pavel Afonine pafonine at lbl.gov
Fri Apr 1 16:16:16 PDT 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<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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