[phenixbb] Changing the resolution cutoff for water picking
Pavel Afonine
PAfonine at lbl.gov
Thu Sep 10 12:06:59 PDT 2009
Hi Sam,
- a quick solution would be to switch to individual ADP refinement,
which is I don't see "why not" at this resolution and R-factors. To do
so, just replace "group_adp" in your "strategy" keyword with
"individual_adp", or simply remove "strategy" completely since the
default is to refine individual coordinates and B-factors.
- I would be interested to know why your original command crashes and to
do so I need to reproduce this crash myself. Could you please send me
the input data and model files (cifs as well) so I can do some debugging?
Thanks!
Pavel.
On 9/10/09 11:55 AM, Sam Stampfer wrote:
> I got past that error but here's what I just ran into. The file ran
> for at least 15 minutes before crashing. The end of the logfile is:
>
> ----------group isotropic ADP
> refinement----------
>
> |-group b-factor refinement (macro cycle = 0; iterations =
> 0)-----------------|
> | r_work = 0.2554 r_free = 0.3100 target = 1.231881 convergence test =
> off |
> |-----------------------------------------------------------------------------|
> approx_equal eps: 1e-06
> approx_equal multiplier: 10000000000.0
> 0.24634187642 approx_equal ERROR
> 0.246340873912 approx_equal ERROR
>
> Traceback (most recent call last):
> File
> "/usr/local/phenix/phenix-1.4-160/phenix/phenix/command_line/refine.py",
> line 11, in <module>
> command_line.run(command_name="phenix.refine", args=sys.argv[1:])
> File
> "/usr/local/phenix/phenix-1.4-160/phenix/phenix/refinement/command_line.py",
> line 89, in run
> call_back_handler=call_back_handler)
> File
> "/usr/local/phenix/phenix-1.4-160/phenix/phenix/refinement/driver.py",
> line 1108, in run
> call_back_handler = call_back_handler)
> File
> "/usr/local/phenix/phenix-1.4-160/phenix/phenix/refinement/strategies.py",
> line 614, in refinement_machine
> h_params = h_params)
> File
> "/usr/local/phenix/phenix-1.4-160/cctbx_project/mmtbx/refinement/adp_refinement.py",
> line 204, in __init__
> log = log)
> File
> "/usr/local/phenix/phenix-1.4-160/cctbx_project/mmtbx/refinement/group.py",
> line 108, in __init__
> assert approx_equal(rwork, fmodel_copy.r_work())
> AssertionError
>
> The .csh file I'm running is called run_min_H2O_solventparams_160.csh
> (though it does not reference solvent.params since that didn't work
> for me):
>
> #!/bin/csh -f
>
> phenix.refine ss46_p3_cv.mtz ss46_rebuilt.pdb \
> output.prefix=results/ss46_rebuilt_min_H2O_solventparams_160 \
> strategy=individual_sites+group_adp \
> cif_link.params nag-nag.cif \
> refinement.ordered_solvent.low_resolution=3.0 \
> twin_law="h,-h-k,-l" \
> ordered_solvent=True
>
> cif_link.params has never caused any problems and it contains the
> following:
>
> refinement.pdb_interpretation.apply_cif_link {
> data_link = NAG-ASN
> residue_selection_1 = chain M and resname NAG and resid 1141
> residue_selection_2 = chain A and resname ASN and resid 141
> }
>
> refinement.pdb_interpretation.apply_cif_link {
> data_link = NAG-ASN
> residue_selection_1 = chain R and resname NAG and resid 1141
> residue_selection_2 = chain D and resname ASN and resid 141
> }
>
> refinement.pdb_interpretation.apply_cif_link {
> data_link = NAG-ASN
> residue_selection_1 = chain M and resname NAG and resid 1398
> residue_selection_2 = chain A and resname ASN and resid 398
> }
>
> refinement.pdb_interpretation.apply_cif_link {
> data_link = NAG-ASN
> residue_selection_1 = chain P and resname NAG and resid 1398
> residue_selection_2 = chain B and resname ASN and resid 398
> }
>
> refinement.pdb_interpretation.apply_cif_link {
> data_link = NAG-ASN
> residue_selection_1 = chain Q and resname NAG and resid 1398
> residue_selection_2 = chain C and resname ASN and resid 398
> }
>
> refinement.pdb_interpretation.apply_cif_link {
> data_link = NAG-ASN
> residue_selection_1 = chain R and resname NAG and resid 1398
> residue_selection_2 = chain D and resname ASN and resid 398
> }
>
> refinement.pdb_interpretation.apply_cif_link {
> data_link = NAG-ASN
> residue_selection_1 = chain M and resname NAG and resid 1430
> residue_selection_2 = chain A and resname ASN and resid 430
> }
>
> refinement.pdb_interpretation.apply_cif_link {
> data_link = NAG-ASN
> residue_selection_1 = chain Q and resname NAG and resid 1430
> residue_selection_2 = chain C and resname ASN and resid 430
> }
>
> refinement.pdb_interpretation.apply_cif_link {
> data_link = NAG-ASN
> residue_selection_1 = chain R and resname NAG and resid 1430
> residue_selection_2 = chain D and resname ASN and resid 430
> }
>
> refinement.pdb_interpretation.apply_cif_link {
> data_link = NAG-ASN
> residue_selection_1 = chain P and resname NAG and resid 1674
> residue_selection_2 = chain B and resname ASN and resid 674
> }
>
> refinement.pdb_interpretation.apply_cif_link {
> data_link = NAG-ASN
> residue_selection_1 = chain Q and resname NAG and resid 1674
> residue_selection_2 = chain C and resname ASN and resid 674
> }
>
> refinement.pdb_interpretation.apply_cif_link {
> data_link = NAG-ASN
> residue_selection_1 = chain R and resname NAG and resid 1674
> residue_selection_2 = chain D and resname ASN and resid 674
> }
>
> nag-nag.cif has also not caused any problems and it contains:
>
> #
> data_link_NAG-NAG
> #
> loop_
> _chem_link_bond.link_id
> _chem_link_bond.atom_1_comp_id
> _chem_link_bond.atom_id_1
> _chem_link_bond.atom_2_comp_id
> _chem_link_bond.atom_id_2
> _chem_link_bond.type
> _chem_link_bond.value_dist
> _chem_link_bond.value_dist_esd
> NAG-NAG 1 O4 2 C1 single 1.4 0.020
> loop_
> _chem_link_angle.link_id
> _chem_link_angle.atom_1_comp_id
> _chem_link_angle.atom_id_1
> _chem_link_angle.atom_2_comp_id
> _chem_link_angle.atom_id_2
> _chem_link_angle.atom_3_comp_id
> _chem_link_angle.atom_id_3
> _chem_link_angle.value_angle
> _chem_link_angle.value_angle_esd
> NAG-NAG 1 O4 2 C1 2 O5 108.700 3.000
> NAG-NAG 1 C4 1 O4 2 O5 112.300 3.000
> #
>
> Thanks for your help!
> -Sam
>
>
> On Thu, Sep 10, 2009 at 1:10 PM, Pavel Afonine <PAfonine at lbl.gov
> <mailto:PAfonine at lbl.gov>> wrote:
>
> Hi Sam,
>
>
>> I'm refining a 2.88 resolution structure and would like to pick
>> waters. I assume the default low_resolution is set to 2.8
>> Angstroms and so my lower resolution map is not yielding any waters.
>
> Yes, this is correct.
>
>> How do I change the resolution cutoff for water picking to be 3.0
>> Angstroms? I tried adding
>> "refinement.ordered_solvent.low_resolution=3.0" to my command
>> line arguments
>
> This is exactly what you need to do.
>
>
>> and phenix is reading this, but the refinement crashes about 15
>> seconds in with the message:
>>
>>
>> ================== Extract refinement strategy and selections
>> =================
>>
>> Sorry: Selection string 'water' results in empty selection
>> (selects no atoms).
>
> I can't tell anything based on the above error message. Can you
> send me the exact command you used including all parameter files
> (if any)?
>
> Pavel.
>
>
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