[phenixbb] AutoSol Br SAD/MAD

Tom Terwilliger tterwilliger at newmexicoconsortium.org
Mon Mar 12 12:31:21 PDT 2018

Hi Ian,

Your critical anomalous stats are:

1. CC-1/2 ... half-dataset correlation for a SAD dataset.  Should be above
about 0.3 in resolution range of interest. You can calculate this with

2. Anomalous correlation between wavelengths.  You get this if you run
phenix.autosol with MAD data and look at the scaling log file. It will
llist each pair-wise comparison of wavelengths and a resolution breakdown
of CC values. Again, looking for 0.3 between peak and remote to indicate
that data are strong to a particular resolution.

3.  If you have independent data sets (different anomalous atom for
example), and each one has a "solution", you can often get a very good idea
of whether both are correct by calculating the map-map correlation
(phenix.get_cc_mtz_mtz). If one is wrong, you get a low value (like 0.05);
this tells you nothing. If the datasets are really the same you may get a
very high number like 0.7 and that tells you nothing as well. But if both
are right, and they are independent, you might get a value like 0.2 - 0.5.
This is very encouraging if you get it.  You can use this trick for all
kinds of structure solution tries and you can automate it to compare
everything in sight. The key is independence...

AutoSol won't really let you choose the number of sites...even if you tell
it 5, it will look for more.

I'd say...always try hard with existing data and if you have the
opportunity to get SeMet data, pursue that in parallel until you get it or
you solve the structure with existing data.

All the best,
Tom T

On Mon, Mar 12, 2018 at 1:17 PM, Ian Slaymaker <iscrystallo at gmail.com>

> Hello Phenixbb,
> I've been out of the crystallography game for a few years and was hoping
> for some suggestions.
> I'm trying to phase a structure (~1200aa protein:DNA complex) with native
> data out to 2.0A and SAD/MAD data out to 3.0-2.6. I'm trying to use Br/I
> soaking while I wait for Sel-Met crystals to grow.
> I'm collecting 1800 frames at a synchrotron and scaling together multiple
> MAD wavelength sets (30 degree inverse wedges) collected from the same
> crystal with phenix.scale_and_merge to achieve >85% anomalous data
> (determined by xtriage). Anomalous signal of the merged data is around 10
> at the 3.5 angstrom shell. I'm keeping an eye on the merging statistics,
> but I'm not sure what the critical stats to monitor are.
> AutoSol has given me a a few possible solutions, finding between 3 and 8
> sites for MAD and SAD sets(I'm letting AutoSol decide how many to find)
> with Resolve Rfactors around 0.34, but low map skew (<1 and sometimes
> negative). I've tried using the initial sites to search for additional Br
> sites, but with no luck, and the density isn't good enough to build
> anything into. I'm doing hyss searches with various resolution cutoffs and
> continue to get the same/similar uninterpretable density with very few
> heavy atom sites found.
> My questions:
> What are the critical stats to look at when merging data for anomalous
> signal?
> Are there parameters to explore in AutoSol to identify more heavy atom
> sites?
> Should I accept that I need to wait for new crystals to grow or keep
> charging ahead with this data, encouraged by some promising numbers by
> AutoSol?
> Thank you in advance for the suggestions.
> -Ian
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Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0033
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