Hi Fulvio,<div><br></div><div>I&#39;m sorry that you&#39;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">&lt;<a href="mailto:fulvio.saccoccia@uniroma1.it" target="_blank">fulvio.saccoccia@uniroma1.it</a>&gt;</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">&gt; Hi Fulvio,<br>
&gt;<br>
&gt;<br>
&gt; The crash in phenix.den_refine that you are seeing is because you do<br>
&gt; not have individual_sites active in your refinement parameters. If you<br>
&gt; change your den.params file to read:<br>
&gt;<br>
&gt;<br>
&gt; refine {<br>
&gt;     strategy = *individual_sites rigid_body individual_adp \<br>
&gt;     group_adp tls occupancies group_anomalous *den<br>
&gt;   }<br>
&gt;<br>
&gt;<br>
&gt; the refinement should work just fine.<br>
&gt;<br>
&gt;<br>
&gt; I will add a check to make sure that this behavior is more clear.<br>
&gt;<br>
&gt;<br>
&gt; Thanks,<br>
&gt; Jeff<br>
&gt;<br>
&gt; On Mon, Sep 3, 2012 at 1:10 AM, fulvio saccoccia<br>
&gt; &lt;<a href="mailto:fulvio.saccoccia@uniroma1.it">fulvio.saccoccia@uniroma1.it</a>&gt; wrote:<br>
&gt;         Dear Phenix users,<br>
&gt;<br>
&gt;                 here you have an error occurred during a DEN<br>
&gt;         refinement cycle on a<br>
&gt;         twinned structure. Please, help me in order to overcome the<br>
&gt;         problem.<br>
&gt;<br>
&gt;         This is the command line I used to run phenix:<br>
&gt;         phenix.den_refine data.mtz model.pdb twin_law=h,-k,-l<br>
&gt;         output.prefix=DEN10 --overwrite main.ncs=true set_b_iso=50<br>
&gt;         convert_to_isotropic=true xray_data.high_resolution=3.6<br>
&gt;         nproc=4<br>
&gt;         secondary_structure_restraints=true optimize_xyz_weight=true<br>
&gt;         optimize_adp_weight=true reference_model.file=3ZVJ-coot1.pdb<br>
&gt;         use_geometry_restraints=true den.params fix_rotamers=true<br>
&gt;<br>
&gt;         den.params is attached<br>
&gt;<br>
&gt;         I was running phenix dev-1145 on a 64bit Debian machine.<br>
&gt;<br>
&gt;         This is the error message:<br>
&gt;<br>
&gt;         Running DEN torsion optimization on 4 processors...<br>
&gt;         Running torsion simulated annealing<br>
&gt;           ...trying gamma 0.0, weight 100.0<br>
&gt;           ...trying gamma 0.2, weight 100.0<br>
&gt;           ...trying gamma 0.0, weight 300.0<br>
&gt;           ...trying gamma 0.2, weight 300.0<br>
&gt;         Traceback (most recent call last):<br>
&gt;           File<br>
&gt;         &quot;/usr/local/phenix-dev-1145/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/den_refine.py&quot;, line 21, in &lt;module&gt;<br>
&gt;             den_refine.run(command_name=&quot;phenix.den_refine&quot;,<br>
&gt;         args=sys.argv[1:])<br>
&gt;           File<br>
&gt;         &quot;/usr/local/phenix-dev-1145/phenix/phenix/refinement/den_refine.py&quot;,<br>
&gt;         line 113, in run<br>
&gt;             customized_master_params=master_phil)<br>
&gt;           File<br>
&gt;         &quot;/usr/local/phenix-dev-1145/phenix/phenix/refinement/command_line.py&quot;,<br>
&gt;         line 146, in run<br>
&gt;             call_back_handler=call_back_handler)<br>
&gt;           File<br>
&gt;         &quot;/usr/local/phenix-dev-1145/phenix/phenix/refinement/driver.py&quot;,<br>
&gt;         line 1532, in run<br>
&gt;             ncs_manager             = self.ncs_manager)<br>
&gt;           File<br>
&gt;         &quot;/usr/local/phenix-dev-1145/phenix/phenix/refinement/strategies.py&quot;,<br>
&gt;         line 830, in refinement_machine<br>
&gt;             log=log)<br>
&gt;           File<br>
&gt;         &quot;/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py&quot;, line<br>
&gt;         88, in __init__<br>
&gt;             &quot;serious error; please contact <a href="mailto:bugs@phenix-online.org">bugs@phenix-online.org</a>.&quot;) %<br>
&gt;         so)<br>
&gt;         RuntimeError: DEN weight optimization failed:<br>
&gt;         DEN cycle 1<br>
&gt;         rfree at start of SA cycle: 0.4642<br>
&gt;         k_rep = 1.00<br>
&gt;         tardy_tree summary:<br>
&gt;           number of vertices: 16570<br>
&gt;           number of edges: 16855<br>
&gt;           find cluster loops: 0 repeats<br>
&gt;           number of fixed vertex lists: 0<br>
&gt;           number of fixed vertices: 0<br>
&gt;           number of clusters: 7857<br>
&gt;           merge clusters with multiple connections: 1 pass<br>
&gt;           number of hinge edges: 7857<br>
&gt;           number of loop edges: 0<br>
&gt;           number of loop edge bendings: 0<br>
&gt;           number of fixed hinges: 0<br>
&gt;<br>
&gt;         CAUGHT EXCEPTION: (argument #0)<br>
&gt;         ARGUMENT LEADING TO EXCEPTION: (0.0, 100.0)<br>
&gt;         Traceback (most recent call last):<br>
&gt;           File<br>
&gt;         &quot;/usr/local/phenix-dev-1145/cctbx_project/libtbx/easy_mp.py&quot;,<br>
&gt;         line 155, in __call__<br>
&gt;             result = O.func(arg)<br>
&gt;           File<br>
&gt;         &quot;/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py&quot;, line<br>
&gt;         227, in try_den_weight_torsion<br>
&gt;             call_back_after_step=False)<br>
&gt;           File<br>
&gt;         &quot;/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py&quot;,<br>
&gt;         line 228, in run<br>
&gt;             reduced_geo_manager=reduced_geo_manager)<br>
&gt;           File<br>
&gt;         &quot;/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py&quot;,<br>
&gt;         line 86, in __init__<br>
&gt;             O.weights = target_weights.xyz_weights_result<br>
&gt;         AttributeError: &#39;NoneType&#39; object has no attribute<br>
&gt;         &#39;xyz_weights_result&#39;<br>
&gt;<br>
&gt;         This is a serious error; please contact<br>
&gt;         <a href="mailto:bugs@phenix-online.org">bugs@phenix-online.org</a>.<br>
&gt;<br>
&gt;         Thanks in advance<br>
&gt;<br>
&gt;         Fulvio Saccoccia<br>
&gt;         PhD student<br>
&gt;         Dept. of Biochemical Sciences<br>
&gt;         Sapienza University of Rome<br>
&gt;         <a href="tel:%2B390649910556" value="+390649910556">+390649910556</a><br>
&gt;<br>
&gt;<br>
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&gt;<br>
&gt;<br>
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</div></div></blockquote></div><br></div>