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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