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Hi Sam,<br>
<br>
- 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.<br>
<br>
- 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?<br>
<br>
Thanks!<br>
Pavel.<br>
<br>
<br>
On 9/10/09 11:55 AM, Sam Stampfer wrote:
<blockquote
cite="mid:80e4ac3c0909101155h1cfc6b05k74fa752cb2c5230a@mail.gmail.com"
type="cite">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 moz-do-not-send="true"
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>
</blockquote>
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