Dear Milya!
I had this problem before to. This was showing active site ligands from the
same view (i.e. after superposition of totally diffeent crystals).
You can use the superposition matrix fom your PDB superposition and apply it
using the program MAPROT in the "INVERT" mode and using "SYMMETRY P1"
as spacegroup to your map.
Matthias
PS: Here is the answer from Ingo I got a that time:
in maprot, you need to always give symmetry P1. if it is between two
very similar cells you will not notice that the density is a little bit
offset, but it starts if they are non-isomorphous crystals, and even
worse so, if different space groups.
cannibalize the following script (which is part of our automagic
pipeline, i will leave fixing up the details, variables and file names
to you), if you like.
cheers
ingo
################################################
#####################
######### rotating maps onto reference structure
####################
################################################
#####################
#
# ... calculate 2fofc and fofc map suitable for rotating
#
fft \
HKLIN $finalmtz \
MAPOUT $TMPDIR/mapout.fft_final2fofc.map.$run << eof-fft >>
cxap_deposit.out.$run
title 2FO-1FC
labin -
F1 = FWT -
PHI = PHWT
xyzlim 0.0 1.0 0.0 1.0 0.0 1.0
end
eof-fft
#
fft \
HKLIN $finalmtz \
MAPOUT $TMPDIR/mapout.fft_finalfofc.map.$run << eof-fft >>
cxap_deposit.out.$run
title 1FO-1FC
labin -
F1 = DELFWT -
PHI = PHDELWT
xyzlim 0.0 1.0 0.0 1.0 0.0 1.0
end
eof-fft
#
#
#
ncsmask \
XYZIN $referencepdb \
MSKOUT $TMPDIR/mapout.mapmask_referencepdb.map.$run << eof-
ncsmask >>
cxap_deposit.out.$run
radius 5.0
eof-ncsmask
#
xlim=`egrep -A1 "After trim:" cxap_deposit.out.$run | tail -1 | awk
'{printf("%5i%5i",$2,$4)}'`
ylim=`egrep -A2 "After trim:" cxap_deposit.out.$run | tail -1 | awk
'{printf("%5i%5i",$2,$4)}'`
zlim=`egrep -A3 "After trim:" cxap_deposit.out.$run | tail -1 | awk
'{printf("%5i%5i",$2,$4)}'`
gridwork=`grep "Grid sampling" cxap_deposit.out.$run | tail -1 | awk
'{print $8, $9, $10}'`
cellwork=`grep "Cell dimensions" cxap_deposit.out.$run | tail -1 | awk
'{print $4, $5, $6, $7, $8, $9}'`
#
# ... the operator obtained above has to be inverted, since we do need
the 'fetching' operator
# here, not the 'putting' one
#
# ... symmetry of the resulting map must be P1, since, of course,
nothing at all would square
# out, if you move the molecule but maintain the original cell
#
maprot \
MAPIN $TMPDIR/mapout.fft_final2fofc.map.$run \
MSKIN $TMPDIR/mapout.mapmask_referencepdb.map.$run \
WRKOUT $rot2fofc << eof-maprot >> cxap_deposit.out.$run
mode from
symmetry P1
average
rota matrix $row1 $row2 $row3
trans $row4
invert
eof-maprot
#
#
maprot \
MAPIN $TMPDIR/mapout.fft_finalfofc.map.$run \
MSKIN $TMPDIR/mapout.mapmask_referencepdb.map.$run \
WRKOUT $rotfofc << eof-maprot >> cxap_deposit.out.$run
mode from
symmetry P1
average
rota matrix $row1 $row2 $row3
trans $row4
invert
eof-maprot
#
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