[phenixbb] Maximum-likelihood score calculation

Nathaniel Echols nechols at lbl.gov
Fri Jul 11 15:41:52 PDT 2014

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

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