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:<br><br><div style="margin-left: 40px;"> ----------group isotropic ADP refinement---------- <br>
<br>|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|<br>| r_work = 0.2554 r_free = 0.3100 target = 1.231881 convergence test = off |<br>|-----------------------------------------------------------------------------|<br>
approx_equal eps: 1e-06<br>approx_equal multiplier: 10000000000.0<br>0.24634187642 approx_equal ERROR<br>0.246340873912 approx_equal ERROR<br><br>Traceback (most recent call last):<br> File "/usr/local/phenix/phenix-1.4-160/phenix/phenix/command_line/refine.py", line 11, in <module><br>
command_line.run(command_name="phenix.refine", args=sys.argv[1:])<br> File "/usr/local/phenix/phenix-1.4-160/phenix/phenix/refinement/command_line.py", line 89, in run<br> call_back_handler=call_back_handler)<br>
File "/usr/local/phenix/phenix-1.4-160/phenix/phenix/refinement/driver.py", line 1108, in run<br> call_back_handler = call_back_handler)<br> File "/usr/local/phenix/phenix-1.4-160/phenix/phenix/refinement/strategies.py", line 614, in refinement_machine<br>
h_params = h_params)<br> File "/usr/local/phenix/phenix-1.4-160/cctbx_project/mmtbx/refinement/adp_refinement.py", line 204, in __init__<br> log = log)<br> File "/usr/local/phenix/phenix-1.4-160/cctbx_project/mmtbx/refinement/group.py", line 108, in __init__<br>
assert approx_equal(rwork, fmodel_copy.r_work())<br>AssertionError<br></div><br>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):<br>
<br><div style="margin-left: 40px;">#!/bin/csh -f<br><br>phenix.refine ss46_p3_cv.mtz ss46_rebuilt.pdb \<br> output.prefix=results/ss46_rebuilt_min_H2O_solventparams_160 \<br> strategy=individual_sites+group_adp \<br>
cif_link.params nag-nag.cif \<br> refinement.ordered_solvent.low_resolution=3.0 \<br> twin_law="h,-h-k,-l" \<br> ordered_solvent=True<br></div><div style="margin-left: 40px;"><br></div>cif_link.params has never caused any problems and it contains the following:<br>
<br><div style="margin-left: 40px;">refinement.pdb_interpretation.apply_cif_link {<br> data_link = NAG-ASN<br> residue_selection_1 = chain M and resname NAG and resid 1141<br> residue_selection_2 = chain A and resname ASN and resid 141<br>
}<br><br>refinement.pdb_interpretation.apply_cif_link {<br> data_link = NAG-ASN<br> residue_selection_1 = chain R and resname NAG and resid 1141<br> residue_selection_2 = chain D and resname ASN and resid 141<br>}<br><br>
refinement.pdb_interpretation.apply_cif_link {<br> data_link = NAG-ASN<br> residue_selection_1 = chain M and resname NAG and resid 1398<br> residue_selection_2 = chain A and resname ASN and resid 398<br>}<br><br>refinement.pdb_interpretation.apply_cif_link {<br>
data_link = NAG-ASN<br> residue_selection_1 = chain P and resname NAG and resid 1398<br> residue_selection_2 = chain B and resname ASN and resid 398<br>}<br><br>refinement.pdb_interpretation.apply_cif_link {<br> data_link = NAG-ASN<br>
residue_selection_1 = chain Q and resname NAG and resid 1398<br> residue_selection_2 = chain C and resname ASN and resid 398<br>}<br><br>refinement.pdb_interpretation.apply_cif_link {<br> data_link = NAG-ASN<br> residue_selection_1 = chain R and resname NAG and resid 1398<br>
residue_selection_2 = chain D and resname ASN and resid 398<br>}<br><br>refinement.pdb_interpretation.apply_cif_link {<br> data_link = NAG-ASN<br> residue_selection_1 = chain M and resname NAG and resid 1430<br> residue_selection_2 = chain A and resname ASN and resid 430<br>
}<br><br>refinement.pdb_interpretation.apply_cif_link {<br> data_link = NAG-ASN<br> residue_selection_1 = chain Q and resname NAG and resid 1430<br> residue_selection_2 = chain C and resname ASN and resid 430<br>}<br><br>
refinement.pdb_interpretation.apply_cif_link {<br> data_link = NAG-ASN<br> residue_selection_1 = chain R and resname NAG and resid 1430<br> residue_selection_2 = chain D and resname ASN and resid 430<br>}<br><br>refinement.pdb_interpretation.apply_cif_link {<br>
data_link = NAG-ASN<br> residue_selection_1 = chain P and resname NAG and resid 1674<br> residue_selection_2 = chain B and resname ASN and resid 674<br>}<br><br>refinement.pdb_interpretation.apply_cif_link {<br> data_link = NAG-ASN<br>
residue_selection_1 = chain Q and resname NAG and resid 1674<br> residue_selection_2 = chain C and resname ASN and resid 674<br>}<br><br>refinement.pdb_interpretation.apply_cif_link {<br> data_link = NAG-ASN<br> residue_selection_1 = chain R and resname NAG and resid 1674<br>
residue_selection_2 = chain D and resname ASN and resid 674<br>}<br></div><br>nag-nag.cif has also not caused any problems and it contains:<br><br><div style="margin-left: 40px;">#<br>data_link_NAG-NAG<br>#<br>loop_<br>
_chem_link_bond.link_id<br>_chem_link_bond.atom_1_comp_id<br>_chem_link_bond.atom_id_1<br>_chem_link_bond.atom_2_comp_id<br>_chem_link_bond.atom_id_2<br>_chem_link_bond.type<br>_chem_link_bond.value_dist<br>_chem_link_bond.value_dist_esd<br>
NAG-NAG 1 O4 2 C1 single 1.4 0.020<br>loop_<br>_chem_link_angle.link_id<br>_chem_link_angle.atom_1_comp_id<br>_chem_link_angle.atom_id_1<br>_chem_link_angle.atom_2_comp_id<br>_chem_link_angle.atom_id_2<br>
_chem_link_angle.atom_3_comp_id<br>_chem_link_angle.atom_id_3<br>_chem_link_angle.value_angle<br>_chem_link_angle.value_angle_esd<br> NAG-NAG 1 O4 2 C1 2 O5 108.700 3.000<br> NAG-NAG 1 C4 1 O4 2 O5 112.300 3.000<br>
# <br></div><br>Thanks for your help!<br>-Sam<br><br><br><div class="gmail_quote">On Thu, Sep 10, 2009 at 1:10 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:PAfonine@lbl.gov">PAfonine@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div bgcolor="#ffffff" text="#000000">
Hi Sam,<div class="im"><br>
<br>
<blockquote type="cite">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. <br>
</blockquote>
<br></div>
Yes, this is correct. <br><div class="im">
<br>
<blockquote type="cite"> 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 </blockquote>
<br></div>
This is exactly what you need to do.<div class="im"><br>
<br>
<blockquote type="cite">and phenix is reading this, but the refinement crashes
about 15 seconds in with the message: <br>
<br>
<div style="margin-left: 40px;"><br>
================== Extract refinement strategy and selections
=================<br>
<br>
Sorry: Selection string 'water' results in empty selection (selects no
atoms).<br>
</div>
</blockquote>
<br></div>
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)?<br>
<br>
Pavel.<br>
<br>
</div>
</blockquote></div><br>