[phenixbb] AssertionError in refinement
Pavel Afonine
PAfonine at lbl.gov
Sat Oct 4 15:28:21 PDT 2008
Hi Raja,
if this problem still exist in the latest version of PHENIX, then I can
only fix it having your data and model and the exact command you use
(since it's almost impossible to find why it crashes this way without
reproducing the crash locally).
So if it still crashing and you are interested in fixing it, please send
me the data, model and the command. As always, I will keep your data
confidential.
Cheers,
Pavel.
On 9/16/2008 3:34 PM, Raja Dey wrote:
> Dear PhenixBB Members,
> I am getting the following error while I am running the refinement given below: It stopped after a while. I enclosed the last part of the log file.
>
> phenix.refine gat.mtz gat-tlsmd.pdb simulated_annealing=true strategy=rigid_body+individual_sites+group_adp+individual_adp+tls tls.params output.prefix=final_1 --overwrite
>
>
> ================================ ADP refinement ===============================
>
>
> ----------TLS refinement----------
>
> |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
> | r_work = 0.2491 r_free = 0.3251 target = 3.621992 convergence test = off |
> |-----------------------------------------------------------------------------|
> |-group b-factor refinement (macro cycle = 1; iterations = 15)----------------|
> | r_work = 0.2437 r_free = 0.3120 target = 3.588460 convergence test = off |
> |-----------------------------------------------------------------------------|
>
> |-Information about rigid groups----------------------------------------------|
> | Total number of atoms = 1591 Number of rigid groups = 3 |
> | group: start point: end point: |
> | x B atom residue <> x B atom residue |
> | 1: -3.758 92.66 N MET 259 <> 10.389 94.12 CD2 LEU 300 |
> | 2: 14.264 58.92 N ILE 301 <> 1.800 100.80 O THR 315 |
> | 3: 1.098 66.36 N SER 316 <> -10.129 70.49 CE MET 368 |
> |-----------------------------------------------------------------------------|
>
> Traceback (most recent call last):
> File "/usr/local/phenix-1.3b-rc6/phenix/phenix/command_line/refine.py", line 5, in <module>
> command_line.run(command_name="phenix.refine", args=sys.argv[1:])
> File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/command_line.py", line 82, in run
> call_back_after_monitor_collect=call_back_after_monitor_collect)
> File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run
> call_back_after_monitor_collect = call_back_after_monitor_collect)
> File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 549, in refinement_machine
> h_params = h_params)
> File "/usr/local/phenix-1.3b-rc6/mmtbx/mmtbx/refinement/adp_refinement.py", line 153, in __init__
> tools.split_u(fmodels.fmodel_xray().xray_structure, tls_selections, offset)
> File "/usr/local/phenix-1.3b-rc6/mmtbx/mmtbx/tls/tools.py", line 498, in split_u
> assert (u_iso < 0.0).count(True) == 0
> AssertionError
>
>
>
> While I can successfully run similar refinement on another project.
>
> I have another question. Inclusion of individual_adp in strategy increases R and R(free) in one case(2.8 A data), while decreases in another case (3.6 A data). Both are at the final stage of refinement. Is there any explanation?
>
> Looking forward to hearing from you...
> Thanking you in advance...
>
> Raja
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>
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