[phenixbb] cif_as_mtz assertion error
pafonine at lbl.gov
Wed Jun 13 09:54:34 PDT 2012
data sets in PDB are not super clean, for example:
- there is a whole lot of entries labeled as intensities but in fact
amplitudes, same true the other way around;
- some neutron structures annotated as X-ray;
- the worst case (I forgot the PDB id) is the neutron structure called
as X-ray with intensities labeled as amplitudes.
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.
If you really know what you are doing then probably not using
--use-model is totally ok.
On 6/13/12 8:05 AM, Eric Williams wrote:
> Thanks. Good to know it's not just me. :)
> 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.
> Thanks. :)
> On Wed, Jun 13, 2012 at 10:59 AM, Nathaniel Echols <nechols at lbl.gov
> <mailto:nechols at lbl.gov>> wrote:
> On Wed, Jun 13, 2012 at 7:36 AM, Eric Williams
> <ericwilliams at pobox.com <mailto:ericwilliams at pobox.com>> wrote:
> > I'm trying to run phenix.cif_as_mtz on a large number of PDB
> entries, and
> > several entries give me an assertion error. The example below is
> from 8icz,
> > but the error always seems to be the same.
> This is a bug (which one of us will fix ASAP), but if you omit the
> --use-model argument, it should avoid the step that's crashing. I
> haven't come across too many entries in the PDB that actually require
> this, especially among newer structures.
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