[phenixbb] pdb_redo

Ed Pozharski ccp4pozharski at gmail.com
Mon Aug 11 09:31:01 PDT 2014

I believe the intent is to provide electron density maps at the end of pdb_redo re-refinement process.  Recent versions of coot allow direct download of pdb_redo maps and there are also pymol plugins. You could ask Robbie Joosten directly whether your specific intended use of pdb_redo output is kosher.

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<div>-------- Original message --------</div><div>From: Nathaniel Echols <nechols at lbl.gov> </div><div>Date:08/11/2014  11:06 AM  (GMT-05:00) </div><div>To: PC <patrick.cossins at inbox.com> </div><div>Cc: PHENIX user mailing list <phenixbb at phenix-online.org> </div><div>Subject: Re: [phenixbb] pdb_redo </div><div>
</div>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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