Re: [phenixbb] Data processing: exhaustive search?

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. Kay On 16.04.2016 21:18, [email protected] wrote:

Message: 6 Date: Sun, 17 Apr 2016 00:48:31 +0530 From: Kaushik Hatti To: PHENIX user mailing list Subject: [phenixbb] Data processing: exhaustive search? Message-ID: Content-Type: text/plain; charset="utf-8"

Hello,

I have a data set diffracted to 2.7A collected at 1.54 wavelength. The data 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 possible 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: [email protected] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz