[phenixbb] Maximum-likelihood score calculation
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.
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
> 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(
> fmodel = cmdline.fmodel
> tf = fmodel.target_functor(compute_gradients=False)
> score = tf_r.target_work()
> print score
> if (__name__ == "__main__") :
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb