[phenixbb] xtriage reindexing suggestions

Terwilliger, Thomas C terwilliger at lanl.gov
Sat Mar 22 16:12:12 PDT 2014

Hi Peter,

At the moment autosol requires that the datasets all be indexed the same way...

All the best,
Tom T

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Peter Zwart [PHZwart at lbl.gov]
Sent: Friday, March 21, 2014 4:30 PM
To: Todd Jason Green
Cc: phenixbb at phenix-online.org
Subject: Re: [phenixbb] xtriage reindexing suggestions

Hi Todd,

The symmetry operator that would jumble up I+ and I- is
(h,k,l)->(-h,-k,-l) [and symmetry related ones]. Once you provide a
dataset that contain anomalous flags, the ASU is expanded such that
Friedel mates are considered to be independent reflections (i.e.
Friedel symmetry is not part of list of operators). Because of this,
the troublesome situation you describe doesn't happen.

I wouldn't be surprised if autosol does all these things for you btw,
but better confirm with Tom.


On 21 March 2014 15:14, Todd Jason Green <tgreen at uab.edu> wrote:
> Hello all-
> I am trying to merge a few partial Se datasets. I am certain that I will
> have to reindex one or more to make sure that + and - reflections are not
> jumbled up. Can someone confirm that xtriage take this into account in
> suggesting to reindex one dataset in relation to a reference dataset? ie.
> does it use something like maximizing the anomalous signal in suggesting
> whether or not reindexing is necessary? I think the below suggests as much
> but I wanted confirmation:
> Automatic re-indexing
> For each data set supplied (other than the first data set given), all
> possible re-indexing matrices are derived as described by Grosse-Kunstleve
> et al. (2005). Each data set isautomatically re-indexed using the matrix
> that maximizes the correlation of amplitudes
> Have a good weekend.
> -Todd
> My Example:
> Reference analyses
>    The following reindexing operators have been found:
> -------------------------------------------------
> | Operator | Correlation | matches (%) | choice |
> -------------------------------------------------
> | -k,h,l   | 0.874       | 70.1        |  <---  |
> | h,k,l    | 0.032       | 76.7        |        |
> -------------------------------------------------
> If the data is reindexed with operator (-k,h,l), the correlation of
> the intensities to the reference data is maximized.
> sx205b_anom.sca
> This can be done for instance with:
>   phenix.reflection_file_converter sx205b_anom.sca
> --change_of_basis="-k,h,l" <output_options>
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P.H. Zwart
Research Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:      http://bcsb.als.lbl.gov
PHENIX:   http://www.phenix-online.org
SASTBX:  http://sastbx.als.lbl.gov
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