Hi Fulvio,<div><br></div><div>The crash in phenix.den_refine that you are seeing is because you do not have individual_sites active in your refinement parameters. If you change your den.params file to read:</div><div><br></div>
<div><div>refine {</div><div> strategy = *individual_sites rigid_body individual_adp \</div><div> group_adp tls occupancies group_anomalous *den</div><div> }</div><div><br></div><div>the refinement should work just fine.</div>
<div><br></div><div>I will add a check to make sure that this behavior is more clear.</div><div><br></div><div>Thanks,</div><div>Jeff</div><br><div class="gmail_quote">On Mon, Sep 3, 2012 at 1:10 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 Phenix users,<br>
<br>
here you have an error occurred during a DEN refinement cycle on a<br>
twinned structure. Please, help me in order to overcome the 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 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", 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 "/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>.") % 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 "/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 'xyz_weights_result'<br>
<br>
This is a serious error; please contact <a href="mailto:bugs@phenix-online.org">bugs@phenix-online.org</a>.<br>
<br>
Thanks in advance<br>
<span class="HOEnZb"><font color="#888888"><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>
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<br></blockquote></div><br></div>