I understand this surprising feature now ..
The atomic density is being smeared by the BADD 100 to cover a volume >
3A from the atomic centre. (3.2A to be more precise..)
But the limit on the map sections to be included in the inverse fft is
calculated without that BADD - in fact you use the default 2.5A.
This means that an atom on the first section (y=0.0) does not include
the density in sections y=-2.5/NY to -3.2/NY
Hence the peculiarity.
It goes away if you move the atom to (x,y,z) = (0,3,0)
Will try to fix sfall, but for the time being either do not use BADD ,
or move the atom..
Eleanor
Stefano TRAPANI wrote:
Dear CCP4ers
I got some strange output maps from sfall while I was trying to
generate electron density models for a viral particle using its atomic
coordinates.
I systematically observe an unrealistic equatorial valley in the
caculated electron density map:
