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Hi Eric,<br>
<br>
data sets in PDB are not super clean, for example:<br>
<br>
- there is a whole lot of entries labeled as intensities but in fact
amplitudes, same true the other way around;<br>
- some neutron structures annotated as X-ray;<br>
- the worst case (I forgot the PDB id) is the neutron structure
called as X-ray with intensities labeled as amplitudes.<br>
<br>
So, the --use-model option tries to deconvolute these cases simply
by trying all possibilities and scoring the results by R-factor. It
makes phenix.cif_as_mtz to run a bit longer.<br>
<br>
If you really know what you are doing then probably not using
--use-model is totally ok.<br>
<br>
Pavel<br>
<br>
On 6/13/12 8:05 AM, Eric Williams wrote:
<blockquote
cite="mid:CANZF9CVyNezsunnr1GL1Sq_Grj2U-9ygBRVe2+E7vybDdw1V0A@mail.gmail.com"
type="cite">Thanks. Good to know it's not just me. :)
<div><br>
</div>
<div>How might I know which structures do and don't require
--use-model? I'm running cif_as_mtz on the whole PDB so I can
then run model_vs_data. If I know when to use that switch and
when not to, I can mend my script accordingly.</div>
<div><br>
</div>
<div>Thanks. :)</div>
<div><br>
</div>
<div>Eric<br>
<br>
<div class="gmail_quote">On Wed, Jun 13, 2012 at 10:59 AM,
Nathaniel Echols <span dir="ltr"><<a
moz-do-not-send="true" 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 7:36 AM, Eric
Williams <<a moz-do-not-send="true"
href="mailto:ericwilliams@pobox.com">ericwilliams@pobox.com</a>>
wrote:<br>
> I'm trying to run phenix.cif_as_mtz on a large number
of PDB entries, and<br>
> several entries give me an assertion error. The
example below is from 8icz,<br>
> but the error always seems to be the same.<br>
<br>
</div>
This is a bug (which one of us will fix ASAP), but if you
omit the<br>
--use-model argument, it should avoid the step that's
crashing. I<br>
haven't come across too many entries in the PDB that
actually require<br>
this, especially among newer structures.<br>
<br>
-Nat<br>
</blockquote>
</div>
</div>
</blockquote>
<br>
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