[phenixbb] Refining Anomalous Groups

Terwilliger, Thomas C terwilliger at lanl.gov
Tue Nov 20 05:51:59 PST 2012

Hi Nat,

Yes, you're right (I forgot).  For autosol runs with SAD data and where remove_aniso=True, a file  exptl_fobs_phases_freeR_flags_1_with_anom_data_with_hl_anom.mtz is created with the original anomalous data is created. This is suitable for refinement.

And also yes, you're right that it is much better to copy the freeR flags instead of creating a new set which could cause a lot of confusion later.

All the best,
Tom T
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Nathaniel Echols [nechols at lbl.gov]
Sent: Monday, November 19, 2012 10:52 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Refining Anomalous Groups

On Mon, Nov 19, 2012 at 7:47 PM, Terwilliger, Thomas C <terwilliger at lanl.gov<mailto:terwilliger at lanl.gov>> wrote:
I'm sorry, part of the problem is that autosol exptl_fobs_phases_freeR_flags_1.mtz file does not retain the anomalous information.  This is now on my list be fixed (not quickly though because I will be able to do it only when I convert a whole lot of other things).

But doesn't AutoSol write another MTZ file that is anomalous?  In one of my directories I have this:


which definitely has F+ and F-.  (I'm not certain whether this actually appears in the GUI or not - if not, sorry, that's a bug.  And it may not be propagated to other programs either, which could also be misleading.)

So in your case the best thing is to run phenix.refine with your original mtz file.  You can create a freeR set in the GUI.

I wouldn't recommend creating a new test set - it is just as easy to combine the anomalous data from the original MTZ file with the R-free flags from exptl_fobs_phases_freeR_flags_1.mtz in the reflection file editor.

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