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 <[email protected]> wrote:
Hi Sam,Yes, this is correct.
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.
This is exactly what you need to do.
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
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)?
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).
Pavel.