[phenixbb] pdb_redo

Nathaniel Echols nechols at lbl.gov
Mon Aug 11 08:06:26 PDT 2014

On Mon, Aug 11, 2014 at 10:50 AM, PC <patrick.cossins at inbox.com> wrote:

>  I was wondering what the community thought of the use of PDB_REDO for
> MTZ files?
> I see that they have easy to download MTZ files but has anyone actively
> used them?

Unless we're looking at something different, these are output from Refmac,
and do not include all of the data contained in the original deposition.  I
am not sure if the data will have undergone other changes as well.  For
instance, the deposited structure factors for PDB ID 2whz include both the
fully processed anomalous differences (DANO) and the anomalous intensities
(I+/I- and sigmas).  The MTZ file I found on PDB_REDO has neither, just FP
with Friedel mates merged.  This throws out important information.

Personally, I just do this:

phenix.fetch_pdb --mtz 2whz

or this:

phenix.fetch_pdb --maps 2whz

(Perhaps someday we'll have a server for this.)  I should mention however
that this will fail on a significant fraction of PDB entries that do not
adhere to the CIF standard, at least as implemented in CCTBX.

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