<br clear="all"><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse;color:rgb(34,34,34)"><p><font face="arial, helvetica, sans-serif">Claudia Millán (<a href="mailto:cmncri@ibmb.csic.es" style="color:rgb(17,85,204)" target="_blank">cmncri@ibmb.csic.es</a>)</font></p>
<p><font face="arial, helvetica, sans-serif">Institut de Biologia Molecular de Barcelona (IBMB-CSIC)</font></p><p><font face="arial, helvetica, sans-serif">Barcelona, Spain</font></p></span>Hi again :)<div><br></div><div>
Thanks for the piece of code. I was looking at it rigth now and getting it to work, but i got this error:</div><div><br></div><div><div>Traceback (most recent call last):</div><div> File "simple_command_line_cc.py", line 47, in <module></div>
<div> run(sys.argv[1:])</div><div> File "simple_command_line_cc.py", line 31, in run</div><div> prefer_anomalous=False)</div><div>TypeError: __init__() got an unexpected keyword argument 'prefer_anomalous'</div>
<div><br></div><div>I went to my cctbx_sources files, and look for the mmtbx/utils.py, and then realise that on there, the class cmdline_load_pdb_and_data, in is __init__, doesn't expect a prefer_anomalous keyword but a scattering_table one:</div>
<div><br></div><div><div>def __init__ (self, args, master_phil, out=sys.stdout,</div><div> process_pdb_file=True, create_fmodel=True, scattering_table="wk1995")</div></div><div><br></div><div>Guess it maybe something related to the version of the cctbx i'm using?</div>
<br><div class="gmail_quote">2012/10/9 Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On Tue, Oct 9, 2012 at 5:35 AM, Claudia Millán Nebot<br>
<<a href="mailto:cmncri@ibmb.csic.es">cmncri@ibmb.csic.es</a>> wrote:<br>
> Hi Nat, thanks for pointing it out. Actually, i'm preparing this for a small<br>
> example script in order to include it in a practical seminar about the<br>
> features and tools of the cctbx, so it is not that critical, but I would be<br>
> glad to get some example code of how to use it properly, because my plans<br>
> are to deepen into the use of these tools.<br>
<br>
</div>I've attached a template which reads in the model and data, creates<br>
the fmodel object, and calculates CC(obs-calc). This is also in SVN<br>
now under mmtbx/examples/simple_command_line_cc.py, but I'll probably<br>
go back and modify it later to add more examples like calculating the<br>
model-map CC for an atom selection. There are of course other ways to<br>
write this, but it makes maximal use of Pavel's and my code for the<br>
really common, boring tasks like processing reflection files<br>
consistently, so it's a good place to start for writing programs with<br>
similar inputs.<br>
<br>
-Nat<br>
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