In addition to contouring differences, your mapmask script asks for
a border of only 2 A around the pdb file. If you're looking for
waters, unbuilt loops, or things on the edge of your pdb file, this
will need to be larger. When I used O and created the maps over the
pdb file of interest I used a border at least 5 A.
On Feb 14, 2007, at 9:58 AM, mac minista wrote:
Hi,
thank you for your suggestions, the difference I am
seeing in the maps is mainly with the Fo-Fc maps i.e.
what appears in coot does not always appear in
O/Pymol. Here are the scripts for FFT and MAPMASK:
FFT
#!/bin/sh
set -e
fft hklin model.mtz mapout fofc_f.map <<eof
title fofc map
labin F1=FOFCWT PHI=PHFOFCWT
end
eof
#
fft hklin model.mtz mapout 2fofc_f.map <<eof
title 2fofc map
labin F1=2FOFCWT PHI=PH2FOFCWT
end
eof
MAPMASK
#!/bin/sh
set -e
# Run mapmask after fft to extend the map
mapmask mapin fofc_f.map mapout fofc_fext.map \
xyzin model.pdb <<eof
border 2.0
eof
#
mapmask mapin 2fofc_f.map mapout 2fofc_fext.map \
xyzin model.pdb <<eof
border 2.0
eof
I will try and get some figures.
Regards
Mac
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Biochemistry & Biopphysics
University of Arizona
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