[phenixbb] SAD related query

Thomas C. Terwilliger terwilliger at lanl.gov
Tue Sep 4 07:30:44 PDT 2007

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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>> Today's Topics:
>>    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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> --
> Tara Kashav,
> Dr. S. Gourinath's Lab,
> Lab No 430,
> School of Life Sciences,
> Jawaharlal Nehru University,
> New Delhi - 110067
> _______________________________________________
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