Hi Sam, - 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. - 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? Thanks! Pavel. On 9/10/09 11:55 AM, Sam Stampfer wrote:

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 mailto:[email protected]> 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.