Re: [phenixbb] Maximum-likelihood score calculation

11 Jul 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,

Jouko

On Fri, Jul 11, 2014 at 6:03 PM, Nathaniel Echols  wrote:
...
On Fri, Jul 11, 2014 at 2:48 PM, Jouko Virtanen  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:])