On Fri, Jul 11, 2014 at 3:28 PM, Jouko Virtanen <jouko@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