[phenixbb] Data processing: exhaustive search?
hskaushik at gmail.com
Sun Apr 17 05:27:25 PDT 2016
Thanks for the detailed response. I will go through the links including
the book chapter that you pointed to and then decide what next to do
On Sun, Apr 17, 2016 at 2:19 AM, Kay Diederichs <
kay.diederichs at uni-konstanz.de> wrote:
> Hi Kaushik,
> there is no need for, and no sense in, an exhaustive search of data
> processing parameter space, because its dimensionality is way too high
> to achieve anything useful. The programs MOSFLM and XDS have undergone
> decades of development, and their processing defaults are carefully
> chosen. It is rather the user of the programs who is in charge to
> correctly interpret the output (which requires reading of their
> documentation, and some experience), and to make meaningful adjustments
> to (usually very) few parameters.
> Speaking for XDS, I recommend to read XDSwiki articles (there are
> tutorials and example data sets, and lots of explanations) and a book
> chapter that I recently wrote (#131 at
> http://cms.uni-konstanz.de/strucbio/diederichs-group/publications ). If
> you use the generate_XDS.INP script from XDSwiki, and follow the paper
> and the "Optimization" article, you will get good data from XDS. (There
> are other scripts, like autoPROC, xia2, xdsme and so on, which usually
> also give good results but I don't know them well.) In particular, in
> case of XDS there is usually no need to fiddle around with "box size,
> spot separation, tolerance and other parameters".
> The fact that you seem to try and optimize Rmerge suggests to me that
> you are trading precision for accuracy. Too many people still do this,
> but it is a legacy of the past. "Trying a combination of better frames
> over poorer frames" is most likely _not_ going to improve your merged
> intensities - this is another unfortunate and very common
> misunderstanding (see references 113 and 130).
> I hope this helps you to get better data.
> On 16.04.2016 21:18, phenixbb-request at phenix-online.org wrote:
> > Message: 6
> > Date: Sun, 17 Apr 2016 00:48:31 +0530
> > From: Kaushik Hatti <hskaushik at gmail.com>
> > To: PHENIX user mailing list <phenixbb at phenix-online.org>
> > Subject: [phenixbb] Data processing: exhaustive search?
> > Message-ID:
> > <CAGMFGb=B9s-j4yXmRx8_M7NPndf86puviiY9QMg=
> EAqaWr9thw at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> > Hello,
> > I have a data set diffracted to 2.7A collected at 1.54 wavelength. The
> > is not of great quality with very close spots, ellipsoid spots in certain
> > regions of the frames and spot overlaps. Also certain frames are poorer
> > than rest. The crystal could not be reproduced.
> > The best R merge (overall) I have achieved so far is 17% with 85%
> > completeness and 3 I/SigI processed in P4 space group. I feel it's
> > to process it better by identifying right values for box size, spot
> > separation, tolerance and other parameters. I am also suspecting a higher
> > symmetry space group. I believe, trying a combination of better frames
> > over poorer ones with improve merging statistics.
> > I have so far tried processing in iMosflm and XDS. Is there a tool which
> > could search exhaustively trying different values for parameters and
> > suggest the combination which provide best merging statistics?
> > Sorry if this question is not relevant in this group.
> > Any pointers/suggestions would be gratefully helpful.
> > Thanks in advance,
> > Regards,
> > Kaushik
> > Molecular Biophysics Unit,
> > Indian Institute of Science,
> > Bangalore, India.
> Kay Diederichs http://strucbio.biologie.uni-konstanz.de
> email: Kay.Diederichs at uni-konstanz.de Tel +49 7531 88 4049 Fax 3183
> Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz
Stupidity is everyone’s birthright. However, only the learned exercise it!
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