[phenixbb] Maps

mohamed noor mohamed.noor34 at gmail.com
Tue Mar 31 17:19:04 PDT 2015

Dear developers

What is the difference between MEM and FEM maps? I read the documentation
and my understanding is both are supposed to create beautiful maps :)

My problem is I have a structure at 1.9 A (a different protein than the one
referred to in my previous question), the Rfactor is around 20/22 %, Rms
bonds is 0.03 and Rms angles is 1.845. If the bonds/angles get lower, the
Rfactor jumps up (same problem as the other structure).

Looking in Coot, there are positive and negative density and missing
density for the side chains of residues with high B factor. For some
reason, phenix.refine keeps on adding water at strange places even at
regions that I suspect to be just noise. For this reason, I want to see if
the noise is really noise. A second reason is I have density that seem to
be too big for a water molecule but waters were placed anyway, so I want to
know if these are real positive density.

The dataset was obtained from only 50 degrees, SG is P 61 2 2. Including
more images brought up the Rmerge to 30-40% and Rfactor being stuck at 30
%. For some reason, I don't find the X-ray statistics from the
phenix.model_vs_data logfile but in essence, I have:

28-1.9: 82 %
6 A - infinity: 95 %
in the shells (2.25-2.14, 2.14-2.04, 2.04-1.97, 1.97-1.9) my completeness
is around 85-62 % and CCwork is at least 70 % and CC1/2 of the dataset is
60 % at the highest resolution shell.

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