The work-around seems to work...er...around. Thanks. :)<div><br></div><div>Eric<br><br><div class="gmail_quote">On Wed, Jun 13, 2012 at 11:17 AM, 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 class="im">On Wed, Jun 13, 2012 at 8:05 AM, Eric Williams <<a href="mailto:ericwilliams@pobox.com">ericwilliams@pobox.com</a>> wrote:<br>
> How might I know which structures do and don't require --use-model? I'm<br>
> running cif_as_mtz on the whole PDB so I can then run model_vs_data. If I<br>
> know when to use that switch and when not to, I can mend my script<br>
> accordingly.<br>
<br>
</div>Pavel might know this, since he's the person who normally runs this.<br>
Normally, I would also suggest that you take advantage of a resource<br>
in Phenix:<br>
<br>
$PHENIX/chem_data/polygon_data/all_mvd.pickle<br>
<br>
which contains model_vs_data results for all applicable PDB entries.<br>
However, this has not been updated since at least last August, and in<br>
the meantime, there have been thousands of new entries added to the<br>
PDB, plus Pavel recently changed the bulk solvent correction and<br>
scaling procedure, which tends to result in slightly lower R-factors,<br>
so I think it's officially obsolete right now.<br>
<br>
As it happens, phenix.cif_as_mtz appears to offer an additional way<br>
around the crash, which is the argument<br>
"--remove_systematic_absences". �Try adding this to your existing<br>
script (keeping "--use_model") and see if that fixes the problem.<br>
Just to be safe, I would also add "--map_to_asu" (which will move<br>
reflections around so the h,k,l indices are in the canonical setting)<br>
and "--merge" (which will merge non-unique reflections - keeping<br>
Friedel pairs separate, of course). �Looks like we need to update our<br>
documentation.<br>
<div class="HOEnZb"><div class="h5"><br>
-Nat<br>
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</div></div></blockquote></div><br></div>