[phenixbb] SAD related query

Tue Sep 4 10:19:45 PDT 2007

Hi Tara,

sorry for the late reply. Yesterday was a holiday.

I had a look at the mtz file you send me and things are disturbing.

The 'strong' data goes to about 3A, which is not too bad. The data
complete, but the intensity statistics as given by xtriage look really
murky:

-------------------------------------------------------------------------------------------------------------
Twinning and intensity statistics summary (acentric data):

Statistics independent of twin laws
  - <I^2>/<I>^2 : 1.649
  - <F>^2/<F^2> : 0.862
  - <|E^2-1|>   : 0.587
  - <|L|>, <L^2>: 0.382, 0.211
       Multivariate Z score L-test: 13.067
       The multivariate Z score is a quality measure of the given
       spread in intensities. Good to reasonable data is expected
       to have a Z score lower than 3.5.
       Large values can indicate twinning, but small values do not
       neccesarily exclude it.

No (pseudo)merohedral twin laws were found.

Patterson analyses
  - Largest peak height   : 6.820
   (correpsonding p value : 5.346e-01)

The largest off-origin peak in the Patterson function is 6.82% of the
height of the origin peak. No significant pseudotranslation is detected.

The results of the L-test indicate that the intensity statistics
are significantly different then is expected from good to reasonable,
untwinned data.
As there are no twin laws possible given the crystal symmetry, there could be
a number of reasons for the departure of the intensity statistics from
normality.
Overmerging pseudo-symmetric or twinned data, intensity to amplitude
conversion problems
 as well as bad data quality might be possible reasons.
It could be worthwhile considering reprocessing the data.

-------------------------------------------------------------------------------

As your spacegroup is P4322, i suggest you try carefull reprocessing
of your data in P43 to check the intensity statistics in that
spacegroup. You could have data that is merohedrally twinned and you
might have overmerged your data,. This would be possible if twin
fraction is relatively close to 50%.

Furthermore, are you sure about the P43 bit? What about P41?

HTH

Peter

2007/9/4, Thomas C. Terwilliger <terwilliger at lanl.gov>:
> Hi Tara,
>
> It sounds like autosol was not able to find a very good solution to your
> structure.  I would not be too optimistic from what you have said so far,
> but here is a list of things to check over (from the about-to-be-released
> phenix manual...!)
>
> all the best,
> Tom T
>
>
> Autosol SAD tutorial: What to do if I do not get a good solution:
>
> If you do not obtain a good solution, then it's not time to give up yet.
> There are a number of standard things to try that may improve the
> structure determination. Here are a few that you should always try:
>
>     * Have a careful look at all the output files. Work your way through
> the main log file (e.g., AutoSol_run_1_1.log) and all the other
> principal log files in order beginning with scaling
> (dataset_1_scale.log), then looking at heavy-atom searching
> (p9_se_w2_PHX.sca_ano_1.sca_hyss.log), phasing (e.g., phaser_1.log or
> phaser_xx.log depending on which solution xx was the top solution) and
> density modification (e.g., resolve_xx.log). Is there anything strange
> or unusual in any of them that may give you a clue as to what to try
> next? For example did the phasing work well (high figure of merit) yet
> the density modification failed? (Perhaps the hand is incorrect). Was
> the solvent content estimated correctly? (You can specify it yourself
> if you want). What does the xtriage output say? Is there twinning or
> strong translational symmetry? Are there problems with reflections
> near ice rings? Are there many outlier reflections?
>     * Try a different resolution cutoff. For example 0.5 A lower
> resolution than you tried before. Often the highest-resolution shells
> have little useful information for structure solution (though the data
> may be useful in refinement and density modification).
>     * Try a different rejection criterion for outliers. The default is
> ratio_out=3.0 (toss reflections with delta F more than 3 times the rms
> delta F of all reflections in the shell). Try instead ratio_out=5.0 to
> keep almost everything.
>     * If the heavy-atom substructure search did not yield plausible
> solutions, try searching with HYSS using the command-line interface,
> and vary the resolution and number of sites you look for. Can you find
> a solution that has a higher CC than the one found in AutoSol? If so,
> you can read your solution in to AutoSol with sites_file=my_sites.pdb.
>     * Was an anisotropy correction applied in AutoSol? If there is some
> anisotropy but no correction was applied, you can force AutoSol to
> apply the correction with correct_aniso=True.
>
>
>
>
> > Dear all,
> > I am a novice user of phenix.  I am trying to obtain phases for SAD
> > dataset
> > collected at 2.5 angs from autosol.But when i give the phases to
> > autobuild,
> > the R-factor is not decreasing below 49%. Also, in warp, it is unable to
> > built with a message "encounterd an unknown element". Can someone suggest
> > me
> > what could be the problem.
> >
> > Thanks for any suggestion in advance.
> > Tara Kashav
> >
> > On 9/3/07, phenixbb-request at phenix-online.org <
> > phenixbb-request at phenix-online.org> wrote:
> >>
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> >>    1. command-line Patterson maps (Bryan W. Lepore)
> >>
> >>
> >> ----------------------------------------------------------------------
> >>
> >> Message: 1
> >> Date: Sun, 2 Sep 2007 00:07:51 -0500 (CDT)
> >> From: "Bryan W. Lepore" <bryanlepore at mail.utexas.edu>
> >> Subject: [phenixbb] command-line Patterson maps
> >> To: phenixbb at phenix-online.org
> >> Message-ID:
> >>         <
> >> Pine.LNX.4.64.0709020001190.16588 at cpe-70-116-17-26.austin.res.rr.com>
> >> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
> >>
> >> will phenix calculate Pattersons from trial sites or a reflection file
> >> on
> >> the command line?  i.e. something besides hacking what is already there.
> >>
> >> e.g. cns has predict_patterson.inp.  i can't seem to find a way to do it
> >> from the command line - such as `phenix.patterson --sg=94
> >> reflections.mtz`.  i saw phenix.maps but that looks like electron
> >> density
> >> only.
> >>
> >> -bryan
> >>
> >>
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> >> End of phenixbb Digest, Vol 22, Issue 1
> >> ***************************************
> >>
> >
> >
> >
> > --
> > Tara Kashav,
> > Dr. S. Gourinath's Lab,
> > Lab No 430,
> > School of Life Sciences,
> > Jawaharlal Nehru University,
> > New Delhi - 110067
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
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> >
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