[phenixbb] on the Crystallographic data and refinement statistics table in the crystallography paper

[Nathaniel Echols]

On Mon, Apr 30, 2012 at 1:12 AM, Sebastiano Pasqualato
<sebastiano.pasqualato at gmail.com> wrote:
> I just wanted to let you know that when processing the data with XDS (in my
> case with xia2) and providing the CORRECT.LP logfile to phenix.table_one,
> the program fails to extract information on total reflections, multiplicity,
> Rsym.

I could have overlooked something.  Could you please send me the
logfile?  (If you have one that is already published which we could
use for regression testing, even better.)

Does xia2 also extract something of this info automatically, e.g. for
REMARK 200 records?  If Graeme has already done some of the work I
should just figure out how to use that instead of writing yet another
logfile parser - although I guess people use XDS manually too.

> I have a question, too.
> In the case the refinement resolution is different from the integration one,
> would the table give both series of values.

No, the assumption is that these are the same - this might seem a
little unreasonable, but as a reader or reviewer I would want to know
what was the mean I/sigma for the reflections *actually used in
refinement*;.

> I usually put in table 1 also the reflections not used in refinement (i.e.
> the Rfree set number of reflections). Would be nice to have it there.

I could probably find a place to fit this in, although this is the
kind of information that I think is best put in the Methods section
(which Phenix still won't write for you - yet).

-Nat