[phenixbb] Question regarding phenix.fmodel

zhangh1 at umbc.edu zhangh1 at umbc.edu
Mon Apr 25 13:26:29 PDT 2011


According to the instruction, phenix.fmodel was supposed to calculate Fc
only; however, when I try the following 2 scripts, they ended up with
different Fc values (at the same hkl point):

1. phenix.fmodel ${PDB} high_resolution=XX
2. phenix.fmodel ${PDB} ${MTZ}

The instruction says (2) will output Fcalc that will match the set of
Miller indices of the data in reflection_data.mtz file, so I thought 1 and
2 should have the same values at the same hkl points...

One more question about fmodel. I have 2 models with different sizes, and
want to compare their Fc in the same scale. If I use (1), there will be no
scaling by default I think, so the Fc results can be directly compared,
right? (A most direct way would be checking the Fc at h0k0l0 point and see
whether they are proportional to the molecular size, but it seems
phenix.fmodel will ignore this point even I expicitly add it to the MTZ



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