[phenixbb] phenix.automr

Thomas C. Terwilliger terwilliger at lanl.gov
Mon Jul 28 05:40:21 PDT 2008

Dear Ivan,

I'm sorry for the trouble!  The problem is that the autobuild wizard
writes the file overall_best_refine_map_coeffs.mtz for the purpose of
generating map coefficients only.  You only want to look at FP PHIM and
FOMM from that file.  The FC in that file is a dummy column  (and yes, it
is zero in this case. It is the FC from density modification in resolve,
if density modification is carried out.  I will remove this FC column in
future versions as it is too confusing.)

So if you want an FC for your model,  the easiest way is to run
phenix.pdbtools.  See the write up at:


which explains just how to generate FMODEL (which I am assuming is what
you are looking for) including all the terms that you specify that you
want to include.

All the best,
Tom T

> Dear All,
> I am trying to use Phenix AutoMR followed by Autobuild.
> The problem is that in the output file
> "overall_best_refine_map_coeffs.mtz" from Autobuild the Fc values have
> been set to zero.
> The Fc values are not zero in the output file MR.1.mtz coming from
> AutoMR if it may be of help.
> Any suggestion to fix this problem will be appreciated.
> Thank you in advance
> Ivan
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