[cctbxbb] Going from a pdb file to an x_ray_structure object

Claudia Millán Nebot cmncri at ibmb.csic.es
Tue Oct 9 06:24:45 PDT 2012

Hi again :)

Thanks for the piece of code. I was looking at it rigth now and getting it
to work, but i got this error:

Traceback (most recent call last):
  File "simple_command_line_cc.py", line 47, in <module>
  File "simple_command_line_cc.py", line 31, in run
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?

Claudia Millán (cmncri at ibmb.csic.es)

Institut de Biologia Molecular de Barcelona (IBMB-CSIC)

Barcelona, Spain

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

> On Tue, Oct 9, 2012 at 5:35 AM, Claudia Millán Nebot
> <cmncri at 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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