Traceback (most recent call last):

File "simple_command_line_cc.py", line 47, in <module>

run(sys.argv[1:])

File "simple_command_line_cc.py", line 31, in run

prefer_anomalous=False)

TypeError: __init__() got an unexpected keyword argument 'prefer_anomalous'

I went to my cctbx_sources files, and look for the mmtbx/utils.py, and then realise that on there, the class cmdline_load_pdb_and_data, in is __init__, doesn't expect a prefer_anomalous keyword but a scattering_table one:

def __init__ (self, args, master_phil, out=sys.stdout,

process_pdb_file=True, create_fmodel=True, scattering_table="wk1995")

Guess it maybe something related to the version of the cctbx i'm using?

2012/10/9 Nathaniel Echols <nechols@lbl.gov>

On Tue, Oct 9, 2012 at 5:35 AM, Claudia Millán Nebot
<cmncri@ibmb.csic.es> wrote:
> Hi Nat, thanks for pointing it out. Actually, i'm preparing this for a small
> example script in order to include it in a practical seminar about the
> features and tools of the cctbx, so it is not that critical, but I would be
> glad to get some example code of how to use it properly, because my plans
> are to deepen into the use of these tools.

I've attached a template which reads in the model and data, creates
the fmodel object, and calculates CC(obs-calc). This is also in SVN
now under mmtbx/examples/simple_command_line_cc.py, but I'll probably
go back and modify it later to add more examples like calculating the
model-map CC for an atom selection. There are of course other ways to
write this, but it makes maximal use of Pavel's and my code for the
really common, boring tasks like processing reflection files
consistently, so it's a good place to start for writing programs with
similar inputs.

-Nat

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