[phenixbb] XDS files in Phenix

Kay Diederichs Kay.Diederichs at uni-konstanz.de
Fri Jun 10 08:08:00 PDT 2011

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 

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,


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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