[phenixbb] Crash after Torsion Angle Refinement

Pavel Afonine PAfonine at lbl.gov
Wed Oct 7 11:01:55 PDT 2009


Hi Ulrich,

sorry for the problem! It is a known bug and I notified Ralf about it on 
8/19/09.

My guess is that it has something to do with torsion angle dynamics code 
that modifies the geometry restraints manager in-place making it invalid 
for the rest of refinement machinery.

I'm afraid that the only solution for now is to turn the torsion angle 
dynamics off.

Pavel.


On 10/7/09 5:26 AM, Ulrich Baumann wrote:
> Dear Phenix-Gurus,
>
> running Phenix-1.5-2 under RHEL 5, 64 bit I get the following error  
> message -- this appears to occur after the actual torsion angle  
> refinement. Hydrogens were added, custom-defined bonds excluded. Could  
> anybody help me out, please?
> Thanks,
> Ulrich
>
>
>    merge clusters with multiple connections: 1 pass
>
>    suppressing allowed origin shifts: True
>    new target temperature:  2500.00 K
>     step=    1 temperature= 2500.0 rmsd=0.0459 r_work=0.2537 r_free=0.3224
>     step=   25 temperature= 2394.4 rmsd=0.3481 r_work=0.2575 r_free=0.3316
>     step=   50 temperature= 2284.4 rmsd=0.3254 r_work=0.2505 r_free=0.3287
>     step=   75 temperature= 2174.4 rmsd=0.3205 r_work=0.2476 r_free=0.3271
>     step=  100 temperature= 2064.4 rmsd=0.3189 r_work=0.2461 r_free=0.3261
>     step=  125 temperature= 1954.4 rmsd=0.3205 r_work=0.2451 r_free=0.3255
>     step=  150 temperature= 1844.4 rmsd=0.3254 r_work=0.2443 r_free=0.3252
>     step=  175 temperature= 1734.4 rmsd=0.3287 r_work=0.2437 r_free=0.3250
>     step=  200 temperature= 1624.4 rmsd=0.3329 r_work=0.2432 r_free=0.3250
>     step=  225 temperature= 1514.4 rmsd=0.3393 r_work=0.2427 r_free=0.3250
>     step=  250 temperature= 1404.4 rmsd=0.3433 r_work=0.2424 r_free=0.3249
>     step=  275 temperature= 1294.4 rmsd=0.3479 r_work=0.2421 r_free=0.3250
>     step=  300 temperature= 1184.4 rmsd=0.3543 r_work=0.2419 r_free=0.3251
>     step=  325 temperature= 1074.4 rmsd=0.3581 r_work=0.2416 r_free=0.3250
>     step=  350 temperature=  964.4 rmsd=0.3629 r_work=0.2414 r_free=0.3251
>     step=  375 temperature=  854.4 rmsd=0.3687 r_work=0.2413 r_free=0.3251
>     step=  400 temperature=  744.4 rmsd=0.3722 r_work=0.2411 r_free=0.3252
>     step=  425 temperature=  634.4 rmsd=0.3771 r_work=0.2409 r_free=0.3252
>     step=  450 temperature=  524.4 rmsd=0.3819 r_work=0.2408 r_free=0.3252
>     step=  475 temperature=  414.4 rmsd=0.3854 r_work=0.2407 r_free=0.3253
>     step=  500 temperature=  304.4 rmsd=0.3906 r_work=0.2406 r_free=0.3254
>    allowed origin shift velocity corrections applied (magnitudes):
>      n: 501
>      min:  0
>      max:  1.30923e-16
>      mean: 1.24537e-17
>    sum of allowed origin shift velocity corrections (vectors):
>      (0.00000, 0.00000, -0.00000)
>
> ================================ xyz refinement  
> ===============================
>
> Traceback (most recent call last):
>    File  
> "/usr/local/phenix-1.5-2/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-1.5-2/phenix/phenix/refinement/command_line.py",  
> line 89, in run
>      call_back_handler=call_back_handler)
>    File "/usr/local/phenix-1.5-2/phenix/phenix/refinement/driver.py",  
> line 1121, in run
>      call_back_handler       = call_back_handler)
>    File  
> "/usr/local/phenix-1.5-2/phenix/phenix/refinement/strategies.py", line  
> 552, in refinement_machine
>      target_weights_params, main, h_params, log, params)
>    File  
> "/usr/local/phenix-1.5-2/phenix/phenix/refinement/strategies.py", line  
> 839, in __init__
>      minimized = self.minimize()
>    File  
> "/usr/local/phenix-1.5-2/phenix/phenix/refinement/strategies.py", line  
> 918, in minimize
>      h_params                 = self.h_params)
>    File  
> "/usr/local/phenix-1.5-2/cctbx_project/mmtbx/refinement/minimization.py", line  
> 39, in __init__
>      self.regularize_h_and_update_xray_structure()
>    File  
> "/usr/local/phenix-1.5-2/cctbx_project/mmtbx/refinement/minimization.py", line  
> 222, in regularize_h_and_update_xray_structure
>      self.h_params.xh_bond_distance_deviation_limit)
>    File "/usr/local/phenix-1.5-2/cctbx_project/mmtbx/model.py", line  
> 167, in idealize_h
>      for t in self.xh_connectivity_table():
>    File "/usr/local/phenix-1.5-2/cctbx_project/mmtbx/model.py", line  
> 118, in xh_connectivity_table
>      xray_structure = xray_structure).table
>    File "/usr/local/phenix-1.5-2/cctbx_project/mmtbx/model.py", line  
> 47, in __init__
>      xray_structure.sites_cart()).bond_proxies.simple
> AttributeError: 'NoneType' object has no attribute 'simple'
>
>
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