Hi,
I am refining a model in Shelxl and occasionally (and most importantly,
today) get a .fcf file that is rendered in a fashion that I believe is
incorrect. When the problem occurs I get a difference map with negative
peaks centered on most of the atoms. I am enclosing a screen shot of
a representative piece of density.
A map that looks like this could be generated by bad temperature
factor scaling, but I don't know why such scaling would be applied.
I am seeing this today with coot-0.4-pre-1-revision-449 and wincoot
0.3.3. If I use shelxpro to calculate O format DSN6 map files and
look at them in O the maps look fine. Unfortunately shelxpro will not
calculate CCP4 format maps.
The problem is reproducible as long as the same .fcf file is used.
However a pair of .fcf files based on very similar models could contain
one that results in a nice looking map and another with a bad map. For
example, my current problem .fcf is based on a model that differs only
in the deletion of about 15 weak "water" molecules and the addition
of another 15 weak "water" molecules. The R values differ by a few
hundredths of a percent yet the difference maps are radically different.
Any insights into this problem, and hints as to how to control it,
will be appreciated.
Dale Tronrud
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