[phenixbb] HKL_base

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Mon Aug 16 22:44:20 PDT 2010

Hi Ed,

> Curious.  Both phenix.mtz.dump and ccp4 mtzdmp indicate that HKL_base is
> present, yet when you actually look at the headers it's missing.  The
> mtzlib description says that HKL_base will be inserted automatically if
> missing, perhaps this is what happens when mtz file is dumped?

Honestly, I never really understood how the HKL_base mechnism is
supposed to work.
Practically: to my knowledge, you are the first ever to report trouble
reading phenix.refine mtz files. How exactly are you reading them?
Maybe a small adjustment could make your reader work?
We are reading everything through the ccp4 cmtz library, just through
C++ wrappers that hide the technicalities of the C interfaces. Therefore
I think any other program using the cmtz library should also be able
to read our files.
The mtz code used by phenix.refine is in this directory:
The main files are object.h, object.cpp, and __init__.py which
contains a .set_hkl_base() method. 
I guess I could try to assign the H,K,L columns to crystal 1 as Nat
suggested, but nobody knows what problems such a change would
trigger, and it will probably take a decade anyway before the current
implementation is flushed out of the system. I think modifying your
reader to work with our files is the best solution and should be
very easy.


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