[phenixbb] Maximum-likelihood score calculation

Jouko Virtanen jouko at umich.edu
Fri Jul 11 15:28:23 PDT 2014

Thank Nathaniel.  I am still confused.  Do you intend me to copy and paste
the script that you included to a file called score.py.  When I did that I
got the following error message

Syntax error: expected "=", found "__future__" (file "score.py", line 1)
Sorry: score.py is not a valid parameter file.

What are the inputs?  I would think that at a minimum I would have to input
a pdb file, mtz file, fasta file, and an estimate for the rmsd.

Thanks again,


On Fri, Jul 11, 2014 at 6:03 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Fri, Jul 11, 2014 at 2:48 PM, Jouko Virtanen <jouko at umich.edu> wrote:
>> I would like to calculate the maximum-likelihood score given an input
>> structure and an mtz file.  How can I do that?  Thanks in advance.
> Do you just want the ML target function value, i.e. what phenix.refine
> prints out at regular intervals?  In that case, you can use the script
> appended below (run with phenix.python score.py), which is derived from
> $PHENIX/cctbx_project/mmtbx/examples/simple_command_line_cc.py.
> from __future__ import division
> import mmtbx.command_line
> import sys
> def master_phil () :
>   return mmtbx.command_line.generic_simple_input_phil()
> def run (args, out=sys.stdout) :
>   cmdline = mmtbx.command_line.load_model_and_data(
>     update_f_part1_for="map",
>     args=args,
>     master_phil=master_phil(),
>     out=out,
>     process_pdb_file=False,
>     create_fmodel=True)
>   fmodel = cmdline.fmodel
>   tf = fmodel.target_functor(compute_gradients=False)
>   score = tf_r.target_work()
>   print score
> if (__name__ == "__main__") :
>   run(sys.argv[1:])
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