[phenixbb] XDS files in Phenix
kay.diederichs at uni-konstanz.de
Fri Jun 10 10:23:04 PDT 2011
Am 10.06.2011 18:27, schrieb Ralf Grosse-Kunstleve:
> Hi Kay,
> Thanks for the explanations!
> 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!
> We have a simple way of merging symmetry-equivalent observations, which
> is used (for example) when we read unmerged scalepack files.
this sounds useful - where can I see this? If this could be enabled then
there is no reason not to read files of type a) or b) .
> 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!
> I've never been sure about the tradeoff between convenience and
> correctness. We could read this file type and merge the observations
> ourselves, which is convenient, but is the result as good as letting XDS
> (or scalepack or scala) do the merging?
I can only speak for XDS - and that internally does just the obviously
a) reject observations with negative sigma
b) use the standard formulas - see
I'd be surprised if SCALEPACK and SCALA use different formulas.
> 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.
> A reader for this file type has been part of Phenix for many years:
> Does this still look right?
yes - except it should reject observations with negative sigma (maybe
I'm overlooking it) but these probably don't occur in MERGE=TRUE files.
and yes - it seems to check that "MERGE=TRUE" so I guess it will
complain in case a) and b) .
> 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.
> Great to know that you can export to MTZ files; I wasn't aware of this
in fact xdsconv writes the necessary files, and prints a few lines of
output to the screen that just have to be cut-and-pasted to get an MTZ
file. Of course this could also easily be scripted.
> before. This looks like the best option in most cases, since the
> symmetry information is preserved in MTZ files (but not CNS files).
More information about the phenixbb