[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
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
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