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@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.