[phenixbb] Changing the resolution cutoff for water picking

Sam Stampfer Samuel.Stampfer at tufts.edu
Thu Sep 10 11:55:03 PDT 2009


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> 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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