[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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