<div dir="ltr">Hi Eric,<div><br></div><div>We will definitely have a look at model_vs_data speed. </div><div><br></div><div>In the mean time, if you have some Python skills, you may consider looking at a Python pickle file in your Phenix distribution:</div><div>modules/chem_data/polygon_data/all_mvd.pickle.</div><div>It contains various statistics (R-factors, etc, more than 70 characteristics) for ~70 000 pdb files. If what you want to obtain from model_vs_data is present there, you may be able to skip calculations and get the numbers you want.</div><div><br></div><div>If you are interested, I can write a small script illustrating how to get some numbers.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Oct 15, 2017 at 10:10 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@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 text="#000000" bgcolor="#FFFFFF">
Eric,<br>
<br>
I'm sorry it is slow, or slower than you expect. I'm sure
technically it can run up to 10 seconds max per largest structure in
PDB, as advertised in <br>
<br>
<a class="m_5383697979820527684moz-txt-link-freetext" href="http://journals.iucr.org/d/issues/2013/04/00/dz5273/dz5273.pdf" target="_blank">http://journals.iucr.org/d/<wbr>issues/2013/04/00/dz5273/<wbr>dz5273.pdf</a><br>
<br>
if corresponding code is appropriately refactored (making most use
of above paper); plus time taken by phenix.molprobity. <br>
<br>
Unfortunately, I'm away till October 26, and then will be at the
workshop till November 6th. <br>
<br>
Others from the team (Dorothee, Oleg, Nigel, Billy, Vincent, Chris?)
are encouraged to feel free to volunteer to address obvious runtime
bottlenecks in this code.<br>
<br>
All the best,<br>
Pavel<span class=""><br>
<br>
<div class="m_5383697979820527684moz-cite-prefix">On 10/15/17 04:35, Eric Williams wrote:<br>
</div>
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<div style="font-family:sans-serif;font-size:13.696px" dir="auto">
<div style="margin:16px 0px">
<div dir="ltr">I'm having a devil of a time getting
model_vs_data to run in a timely fashion. Running the
latest stable Linux build on Ubuntu 14.04 takes on the
order of 3 minutes per structure. That wouldn't be so bad
if I weren't trying to run it on every entry in the PDB.
Is it just a limitation of Python? SFCheck, which I think
is written mostly in FORTRAN, runs in a few seconds. Any
help anyone could offer would be appreciated. Thanks. :)</div>
<div dir="ltr"><font color="#888888"><br>
</font></div>
<div dir="ltr"><font color="#888888">Eric</font><br>
</div>
</div>
</div>
</div>
</blockquote>
<br>
</span></div>
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