Jacob Corn wrote:
This question was posted by someone else in January, but no solution was
ever described. I'm currently running up against the same problem and
would very much like to know if there is a solution, or if I'm stuck in
bug-land.
I have several CCP4 maps that have been calculated over the entire unit
cell (using ccp4's "extend") that can be read in, but only displayed in
a rectangle covering ~1/3 of the unit cell. Unfortunately, my molecule
does not lie within that 1/3. Converting the ccp4 maps to other formats
(xplor, omap, etc.) does not solve the problem.
Is there a way to get pymol to re-center the contouring around my
molecule? Trying to use isomesh or the density wizard to carve around
selections only results in "Surface generated using 0 lines". Putting up
the entire map shows the aforementioned rectangle.
Why are unit-cell-wide maps only displayed over part of the unit cell?
Jacob
Hi Jacob -
Here's my jiffy for making a CCP4-format map covering the molecule.
There are three steps (repeated for the 2Fo-Fc and Fo-Fc maps): using
fft to calculate the maps in an asymmetric unit, using mapmask to move
the map to cover the molecule (with a 6 A cushion), and using mapman (an
Uppsala Software Factory program - thanks Gerard!) to normalize the
maps. Skip any step that seems superfluous...
#!/bin/csh -f
set outmtz='mlsg_refmac_cycle4e.mtz'
set crdout='mlsg_refmac_cycle4e.pdb'
set fftspc=1
set maproot1='map_cycle4e_2fofc'
set maproot2='map_cycle4e_fofc'
set reso='20 1.3'
# Sigmaa style 2mfo-dfc map
#
fft hklin $outmtz mapout $CCP4_SCR/map_2fofcwt.map << eof
title Sigmaa style 2mfo-dfc map calculated with refmac coefficients
labi F1=2FOFCWT PHI=PHWT
resolution $reso
fftspg $fftspc
binmapout
end
eof
#
mapmask \
MAPIN $CCP4_SCR/map_2fofcwt.map MAPOUT $maproot1.dn6 \
xyzin $crdout << eof
border 6.0
end
eof
#
# Sigmaa style mfo-dfc map
#
fft hklin $outmtz mapout $CCP4_SCR/map_fofcwt.map <<eof
title Sigmaa style mfo-dfc map calculated with refmac coefficients
labi F1=FOFCWT PHI=PHDELWT
resolution $reso
fftspg $fftspc
binmapout
end
eof
#
mapmask \
MAPIN $CCP4_SCR/map_fofcwt.map MAPOUT $maproot2.dn6 \
xyzin $crdout << eof
border 6.0
end
eof
#
6d_mapman << eof
read m1 $maproot1.dn6 ccp4
norm m1
write m1 $maproot1.ccp4 ccp4
read m2 $maproot2.dn6 ccp4
norm m2
write m2 $maproot2.ccp4 ccp4
quit
eof
Hope this helps!
- Matt
--
Matthew Franklin Phone:(650)225-4596
Postdoctoral Researcher Fax:(650)225-3734
Genentech, Inc.
1 DNA Way, South San Francisco, CA 94080
