[phenixbb] cif_as_mtz assertion error

Pavel Afonine pafonine at lbl.gov
Wed Jun 13 09:54:34 PDT 2012

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.


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 <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.
>     -Nat

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