<div dir="ltr">Hi Nathaniel,<div><br></div><div>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</div>
<div><br></div><div><div>Traceback (most recent call last):</div><div> File "score.py", line 22, in <module></div><div> run(sys.argv[1:])</div><div> File "score.py", line 9, in run</div><div>
cmdline = mmtbx.command_line.load_model_and_data(</div><div>AttributeError: 'module' object has no attribute 'load_model_and_data'</div></div><div><br></div><div>Thanks,</div><div><br></div><div>Jouko</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Jul 11, 2014 at 6:41 PM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="">On Fri, Jul 11, 2014 at 3:28 PM, Jouko Virtanen <span dir="ltr"><<a href="mailto:jouko@umich.edu" target="_blank">jouko@umich.edu</a>></span> wrote:<br>
</div><div class="gmail_extra"><div class="gmail_quote"><div class="">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">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<div>
<br></div><div>Syntax error: expected "=", found "__future__" (file "score.py", line 1)</div>
<div>Sorry: score.py is not a valid parameter file.</div></div></blockquote><div><br></div></div><div>That's the kind of error message I'd expect if you ran "phenix.refine score.py" instead of "phenix.python score.py".</div>
<div class="">
<div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div>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.</div>
</div></blockquote><div><br></div></div><div>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:</div>
<div><br></div><div>phenix.phaser model.pdb data.mtz seq.fa model_rmsd=1.0 phaser.mode=MR_RNP<br></div><div><br></div><div>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.</div>
<div><br></div><div>-Nat</div></div></div></div>
</blockquote></div><br></div>