Hi Eric,

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.

Pavel

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. :)

Eric

On Wed, Jun 13, 2012 at 10:59 AM, Nathaniel Echols <[email protected]> wrote:
On Wed, Jun 13, 2012 at 7:36 AM, Eric Williams <[email protected]> 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.

-Nat