[phenixbb] XDS files in Phenix

R.M. Garavito garavito at msu.edu
Fri Jun 10 08:24:18 PDT 2011


We have been quite happy using XDS processed data (including twinned,  
SAD, and MAD data) with Phenix via CCP4.  We just process a data set  
through CORRECT, then put the XDS_ASCII.HKL file through Pointless  
(often to reindex different runs or crystals to the same reference  
data set).  We scale the resulting MTZ file with Scala and the MTZ  
file with the merged/scaled data is used as input to Phenix.  It is  
quick (~10-15 min depending) and works fine.  Other then needing 3  
different program suites, I don't see anything wrong with this route  
for routine work.



R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
513 Biochemistry Bldg.
Michigan State University
East Lansing, MI 48824-1319
Office:  (517) 355-9724     Lab:  (517) 353-9125
FAX:  (517) 353-9334        Email:  garavito at msu.edu

On Jun 10, 2011, at 11:08 AM, Kay Diederichs wrote:

> Dear Ralf, dear all,
> Recently there was some discussion about reading of XDS output files  
> here on PhenixBB, and I'd like to try and shed some light on this.
> First, I'm glad to hear this is possible in principle! However, the  
> caveat is, that three types of "native" output files are written by  
> programs from the "XDS program package":
> a) the main program ("xds", or "xds_par") writes only one type of  
> file, called XDS_ASCII.HKL. This has _unmerged_ observations, and  
> this is therefore currently _unsuitable_ for reading by Phenix  
> programs (since the Phenix routine expects merged, unique  
> reflections). If this is nevertheless tried, I see the danger that  
> Phenix might "eat" all observations of a unique reflections except  
> one, possibly without telling about this problem (? - I didn't  
> try!!) - this is definitely not what you want!
> b) the program "xscale" can write an output file with unmerged  
> observations. This is the default, and corresponds to MERGE=FALSE in  
> XSCALE.INP . As for a), this is also not what you want!
> c) the program "xscale" can write an output file with merged  
> observations. This is not the default, but can be obtained by using  
> MERGE=TRUE in XSCALE.INP . This is what you want to read with Phenix  
> programs.
> Thus only possibility c) will give you a "native XDS" file that is  
> ready to be read by Phenix programs.
> In addition to this possibility, one can use of course use "xdsconv"  
> to go from XDS_ASCII.HKL (or any file written by "xscale") to a (non- 
> native XDS) filetype that Phenix programs can read. The most general  
> should be to write a MTZ file, but CNS/X-PLOR type files can also be  
> produced.
> If someone would implement merging of observations in the Phenix  
> routines (it should be straightforward: negative sigmas indicate  
> that observations should not be used; otherwise the standard  
> formulas could be used; symmetry-related reflections of course have  
> to be handled correctly but they are already sorted by unique  
> reflection), then possibilities a) and b) would also work. But until  
> this is implemented, c) should be used.
> Hope this helps,
> Kay
> P.S. The filetypes and everything else around XDS is accurately  
> documented at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/
> -- 
> 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 M647, D-78457 Konstanz
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