[phenixbb] XDS files in Phenix - and why not?

Felix Frolow mbfrolow at post.tau.ac.il
Fri Jun 10 09:15:46 PDT 2011

Well, the little problem arises if one wish to refine a structure with the EXPERIMENTAL data such as intensities. There are dialects ( I presume) between various packages converting intensities to structure factors.
In addition, if the experimental data (such as merged or unmerged SCALEPACK output) is feed into PHENIX it can be used directly for refinement or for the structure determination used on anomalous data or else. Tom will correct me if I am wrong, but there is a local scaling hiding somewhere inside Solve-Resolve which may produce significantly better scaled data. I do not see why the same can not be done with XDS data.
Dr Felix Frolow   
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfrolow at post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Jun 10, 2011, at 18:24 , R.M. Garavito wrote:

> Kay,
> 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.
> Cheers,
> Michael
> ****************************************************************
> 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
>> This e-mail is digitally signed. If your e-mail client does not have the
>> necessary capabilities, just ignore the attached signature "smime.p7s".
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20110610/112033dd/attachment.htm>

More information about the phenixbb mailing list