[phenixbb] Maximum-likelihood score calculation

Jouko Virtanen jouko at umich.edu
Fri Jul 11 16:17:04 PDT 2014

Hi Nathaniel,

I am developing my own MR code.  I want to use the maximum-likelihood score
in phenix as part of an assessment score for the final placed models.  Soon
I will write my own code to calculate the maximum-likelihood score.  Not
having to input a fasta file or rmsd is ok, I just that that it was
mandatory, since there are terms for estimated coordinate error and
incompleteness of the structure in maximum-likelihood score.  You were
right, I did accidentally use phenix.phaser instead of phenix.python.  When
I use phenix.python score.py file.pdb file.mtz (not the actual file paths)
I get the following error message

Traceback (most recent call last):
  File "score.py", line 22, in <module>
  File "score.py", line 9, in run
    cmdline = mmtbx.command_line.load_model_and_data(
AttributeError: 'module' object has no attribute 'load_model_and_data'



On Fri, Jul 11, 2014 at 6:41 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Fri, Jul 11, 2014 at 3:28 PM, Jouko Virtanen <jouko at umich.edu> wrote:
>> 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.
> That's the kind of error message I'd expect if you ran "phenix.refine
> score.py" instead of "phenix.python score.py".
> 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.
> You would definitely need a PDB file and MTZ file - those will just be
> additional command-line arguments.  The script I sent you does not require
> a sequence or estimated RMSD; it also assumes that the model is already
> placed correctly in the unit cell.  Phaser does require the sequence and
> RMSD, however; is that what you really wanted to use?  If you actually need
> to place the model you might as well just run the full Phaser MR_AUTO mode;
> otherwise you can use the MR_RNP mode.  I had expected to be able to do it
> like this:
> phenix.phaser model.pdb data.mtz seq.fa model_rmsd=1.0 phaser.mode=MR_RNP
> although that crashes, which I guess may be a bug.  There are other ways
> to get the same information but it is not clear what exactly you're trying
> to do.
> -Nat
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