[phenixbb] phenix.maps kick maps: seed and error

Nathaniel Echols nechols at lbl.gov
Mon Jul 12 09:40:42 PDT 2010

On Mon, Jul 12, 2010 at 9:20 AM, Alastair Fyfe <afyfe at soe.ucsc.edu> wrote:

> 2) after what appears to be a successful run on a pdb containing two rna
> chains and solvent atoms  I (a) removed all non-RNA atoms and (b) moved all
> RNA atoms to corresponding symmetry locations within the ASU. No other
> changes were involved but I now receive the following python stack trace:
> Compute maps.
> Traceback (most recent call last):
>  File "/home/afyfe/phenix/phenix-1. 6.1-357/cctbx_project/mmtbx/command_line/maps.py",
> line 192, in <module>
>    run(args=sys.argv[1:])
>  File
> "/home/afyfe/phenix/phenix-1.6.1-357/cctbx_project/mmtbx/command_line/maps.py",
> line 168, in run
>    params = params.maps.map_coefficients)
>  File
> "/home/afyfe/phenix/phenix-1.6.1-357/cctbx_project/mmtbx/maps/__init__.py",
> line 295, in __init__
>    coeffs = map_coefficients_from_fmodel(fmodel = fmodel, params = mcp)
>  File
> "/home/afyfe/phenix/phenix-1.6.1-357/cctbx_project/mmtbx/maps/__init__.py",
> line 257, in map_coefficients_from_fmodel
>    average_maps      = False).map_coeffs
>  File
> "/home/afyfe/phenix/phenix-1.6.1-357/cctbx_project/mmtbx/map_tools.py", line
> 73, in __init__
>    map_helper_obj = fmodel.map_calculation_helper()
> AttributeError: 'twin_model_manager' object has no attribute
> 'map_calculation_helper'

I believe kicked maps are incompatible with twinning - this is a
long-standing bug.  The program will automatically apply a twin law if it
thinks this will improve the R-factor (I think it needs to be at least 0.02
lower for this to happen); if you don't think this is appropriate, the
latest version should have a checkbox to disable the twin law.  But if you
really do have twinning, no kick maps.  Sorry!  I will see if I can modify
the code to raise a more useful error message instead of just crashing.

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