[phenixbb] Is the twin refine conflict with order_solvent refine

Pavel Afonine PAfonine at lbl.gov
Tue Aug 4 08:10:46 PDT 2009


Hi Shi Jiahai,

please download and install the latest version from nightly builds:

http://www.phenix-online.org/download/

under "Nightly builds (version 1.4-4 and above)" goto "Latest installers",

and hopefully the problem will go away.

Please let us know if this does not help.

Pavel.


On 8/4/09 6:47 AM, shi jiahai wrote:
> Hi, Dear all,
>
> I am refine a twin dataset with phenix 1.4-3 and CCI (2008_02_08_1610) 
> on a CenOS 5.2 workstation.
>
> When I run refine with twin law or order_solvent alone, the refinement 
> is good. Everything goes smoothly. However if I enable refinement on 
> both twin law and order_solvent, the error comes during the 
> order_solvent refinement as below.
>
> Start model:
>   number           = 55    
>   b_iso_min        = 5.52    (limit = 1.00)
>   b_iso_max        = 60.32   (limit = 60.00)
>   b_iso_mean       = 24.19              
>   anisotropy_min   = 1.00    (limit = 0.10)
>   occupancy_min    = 1.00    (limit = 0.10)
>   occupancy_max    = 1.00    (limit = 1.20)
>   dist_sol_mol_min = 2.13    (limit = 1.80)
>   dist_sol_mol_max = 4.38    (limit = 6.00)
> Traceback (most recent call last):
>   File 
> "/Application/CCI/cci_apps_sources/phenix/phenix/command_line/refine.py", 
> line 5, in <module>
>     command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>   File 
> "/Application/CCI/cci_apps_sources/phenix/phenix/refinement/command_line.py", 
> line 80, in run
>     call_back_after_monitor_collect=call_back_after_monitor_collect)
>   File 
> "/Application/CCI/cci_apps_sources/phenix/phenix/refinement/driver.py", 
> line 1162, in run
>     call_back_after_monitor_collect = call_back_after_monitor_collect)
>   File 
> "/Application/CCI/cci_apps_sources/phenix/phenix/refinement/strategies.py", 
> line 350, in refinement_machine
>     log               = log)
>   File 
> "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py", 
> line 132, in __init__
>     map_cutoff = self.params.primary_map_cutoff).peaks_mapped()
>   File 
> "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py", 
> line 324, in find_peaks
>     log        = self.log)
>   File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/find_peaks.py", 
> line 65, in __init__
>     symmetry_flags    = maptbx.use_space_group_symmetry)
>   File 
> "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py", 
> line 2238, in electron_density_map
>     w2                = w2).fft_map(
>   File 
> "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py", 
> line 2126, in map_coefficients
>     "m_gradient"
> AssertionError
>
>
> Can anybody help me with this? Thanks a lot in advance!
>
> Best Regards,
>
> Shi Jiahai
> Department of Biological Sciences,
> National University of Singapore
>
>  
>
> ------------------------------------------------------------------------
>
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> phenixbb at phenix-online.org
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>   
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