[phenixbb] Death by Big-ass structure

Petrus H Zwart PHZwart at lbl.gov
Wed May 30 15:14:04 PDT 2007

 Hi Ulrich, Frank,

 Ralf has just placed a new version of cci_apps on our download sites
 (www.phenix-online.org). It contains a new application named phenix.xmanip 
(or mmtbx.xmanip if you only download the cctbx). It is basically a rewritten version of
 the reindex.py script I once wrote as an example jiffy.

 xmanip can read in various reflection files or mtz/cns data columns
 which subsequently can be used in reindexing or other tasks.

 The parameter file I send Frank a couple of days ago should still
 work, even though some rearrangements have been made . Typing

 phenix.xmanip reindex.def

 should do the trick. Other options are available as well. One could
 - generate map coefficients from a model (plain FC,PHIC, or sigmaA
   style maps if observed data is available)
 - get anomalous / isomorphous differences
 - scale two datasets together
 - generate symmetry mates of a model
 - the 'custom' option allows you to pass in a snippet of python code
 and have it executed. One has access to all datasets and molecular
 model read in. You could for instance add two datasets or multiply 
 them if it makes you happy.

 Full documentation is under way. If you have any question, please
 let me know.


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