Hi Fulvio,<div><br></div><div>I'm sorry that you're still having trouble. I was able to run a test refinement with your den.params input file when adding individual_sites as a refinement strategy. Can you send me your most recent set of parameters and perhaps any .log file that was generated directly to my email (not the list) and I will take closer look.</div>
<div><br></div><div>Jeff<br><br><div class="gmail_quote">On Tue, Sep 4, 2012 at 4:14 AM, fulvio saccoccia <span dir="ltr"><<a href="mailto:fulvio.saccoccia@uniroma1.it" target="_blank">fulvio.saccoccia@uniroma1.it</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear all,<br>
� � � � I performed den refinement as suggested by Jeff Headd but it does not<br>
work. Just the: phenix.den_refine data.hkl model.pdb (without options at<br>
all for den refinement) works. All attempt to use a den_refine.params<br>
file (edited in such a way that parameters are different from default<br>
ones) were unsuccesful.<br>
<br>
Any advices is welcome<br>
<br>
Thanks<br>
<div class="im HOEnZb"><br>
Fulvio Saccoccia<br>
PhD student<br>
Dept. of Biochemical Sciences<br>
Sapienza University of Rome<br>
<a href="tel:%2B390649910556" value="+390649910556">+390649910556</a><br>
<br>
<br>
<br>
<br>
</div><div class="im HOEnZb">Il giorno lun, 03/09/2012 alle 11.06 -0700, Jeff Headd ha scritto:<br>
</div><div class="HOEnZb"><div class="h5">> Hi Fulvio,<br>
><br>
><br>
> The crash in phenix.den_refine that you are seeing is because you do<br>
> not have individual_sites active in your refinement parameters. If you<br>
> change your den.params file to read:<br>
><br>
><br>
> refine {<br>
> � � strategy = *individual_sites rigid_body individual_adp \<br>
> � � group_adp tls occupancies group_anomalous *den<br>
> � }<br>
><br>
><br>
> the refinement should work just fine.<br>
><br>
><br>
> I will add a check to make sure that this behavior is more clear.<br>
><br>
><br>
> Thanks,<br>
> Jeff<br>
><br>
> On Mon, Sep 3, 2012 at 1:10 AM, fulvio saccoccia<br>
> <<a href="mailto:fulvio.saccoccia@uniroma1.it">fulvio.saccoccia@uniroma1.it</a>> wrote:<br>
> � � � � Dear Phenix users,<br>
><br>
> � � � � � � � � here you have an error occurred during a DEN<br>
> � � � � refinement cycle on a<br>
> � � � � twinned structure. Please, help me in order to overcome the<br>
> � � � � problem.<br>
><br>
> � � � � This is the command line I used to run phenix:<br>
> � � � � phenix.den_refine data.mtz model.pdb twin_law=h,-k,-l<br>
> � � � � output.prefix=DEN10 --overwrite main.ncs=true set_b_iso=50<br>
> � � � � convert_to_isotropic=true xray_data.high_resolution=3.6<br>
> � � � � nproc=4<br>
> � � � � secondary_structure_restraints=true optimize_xyz_weight=true<br>
> � � � � optimize_adp_weight=true reference_model.file=3ZVJ-coot1.pdb<br>
> � � � � use_geometry_restraints=true den.params fix_rotamers=true<br>
><br>
> � � � � den.params is attached<br>
><br>
> � � � � I was running phenix dev-1145 on a 64bit Debian machine.<br>
><br>
> � � � � This is the error message:<br>
><br>
> � � � � Running DEN torsion optimization on 4 processors...<br>
> � � � � Running torsion simulated annealing<br>
> � � � � � ...trying gamma 0.0, weight 100.0<br>
> � � � � � ...trying gamma 0.2, weight 100.0<br>
> � � � � � ...trying gamma 0.0, weight 300.0<br>
> � � � � � ...trying gamma 0.2, weight 300.0<br>
> � � � � Traceback (most recent call last):<br>
> � � � � � File<br>
> � � � � "/usr/local/phenix-dev-1145/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/den_refine.py", line 21, in <module><br>
> � � � � � � den_refine.run(command_name="phenix.den_refine",<br>
> � � � � args=sys.argv[1:])<br>
> � � � � � File<br>
> � � � � "/usr/local/phenix-dev-1145/phenix/phenix/refinement/den_refine.py",<br>
> � � � � line 113, in run<br>
> � � � � � � customized_master_params=master_phil)<br>
> � � � � � File<br>
> � � � � "/usr/local/phenix-dev-1145/phenix/phenix/refinement/command_line.py",<br>
> � � � � line 146, in run<br>
> � � � � � � call_back_handler=call_back_handler)<br>
> � � � � � File<br>
> � � � � "/usr/local/phenix-dev-1145/phenix/phenix/refinement/driver.py",<br>
> � � � � line 1532, in run<br>
> � � � � � � ncs_manager � � � � � � = self.ncs_manager)<br>
> � � � � � File<br>
> � � � � "/usr/local/phenix-dev-1145/phenix/phenix/refinement/strategies.py",<br>
> � � � � line 830, in refinement_machine<br>
> � � � � � � log=log)<br>
> � � � � � File<br>
> � � � � "/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py", line<br>
> � � � � 88, in __init__<br>
> � � � � � � "serious error; please contact <a href="mailto:bugs@phenix-online.org">bugs@phenix-online.org</a>.") %<br>
> � � � � so)<br>
> � � � � RuntimeError: DEN weight optimization failed:<br>
> � � � � DEN cycle 1<br>
> � � � � rfree at start of SA cycle: 0.4642<br>
> � � � � k_rep = 1.00<br>
> � � � � tardy_tree summary:<br>
> � � � � � number of vertices: 16570<br>
> � � � � � number of edges: 16855<br>
> � � � � � find cluster loops: 0 repeats<br>
> � � � � � number of fixed vertex lists: 0<br>
> � � � � � number of fixed vertices: 0<br>
> � � � � � number of clusters: 7857<br>
> � � � � � merge clusters with multiple connections: 1 pass<br>
> � � � � � number of hinge edges: 7857<br>
> � � � � � number of loop edges: 0<br>
> � � � � � number of loop edge bendings: 0<br>
> � � � � � number of fixed hinges: 0<br>
><br>
> � � � � CAUGHT EXCEPTION: (argument #0)<br>
> � � � � ARGUMENT LEADING TO EXCEPTION: (0.0, 100.0)<br>
> � � � � Traceback (most recent call last):<br>
> � � � � � File<br>
> � � � � "/usr/local/phenix-dev-1145/cctbx_project/libtbx/easy_mp.py",<br>
> � � � � line 155, in __call__<br>
> � � � � � � result = O.func(arg)<br>
> � � � � � File<br>
> � � � � "/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py", line<br>
> � � � � 227, in try_den_weight_torsion<br>
> � � � � � � call_back_after_step=False)<br>
> � � � � � File<br>
> � � � � "/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py",<br>
> � � � � line 228, in run<br>
> � � � � � � reduced_geo_manager=reduced_geo_manager)<br>
> � � � � � File<br>
> � � � � "/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py",<br>
> � � � � line 86, in __init__<br>
> � � � � � � O.weights = target_weights.xyz_weights_result<br>
> � � � � AttributeError: 'NoneType' object has no attribute<br>
> � � � � 'xyz_weights_result'<br>
><br>
> � � � � This is a serious error; please contact<br>
> � � � � <a href="mailto:bugs@phenix-online.org">bugs@phenix-online.org</a>.<br>
><br>
> � � � � Thanks in advance<br>
><br>
> � � � � Fulvio Saccoccia<br>
> � � � � PhD student<br>
> � � � � Dept. of Biochemical Sciences<br>
> � � � � Sapienza University of Rome<br>
> � � � � <a href="tel:%2B390649910556" value="+390649910556">+390649910556</a><br>
><br>
><br>
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</div></div></blockquote></div><br></div>