Map set
Jump to navigation
Jump to search
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.
Map_set provides a number of common operations on and between maps. For example, with Map_set you can add two maps together or create a consensus map from a series of maps or even take a difference map.
Usage
map_set name, operator, operands, target_state, source_state
operator may be,
* average * copy * difference * maximum * minimum * sum * unique
Examples
# add 3 maps
map_set my_sum, add, map1 map2 map3
# calculate the average map
map_set my_avg, average, map1 map2 map3
NOTES
source_state = 0 means all states target_state = -1 means current state experimental
Detailed Example
This example shows you how to create a consensus map of the bound ligand in a conserved pocket.
# fetch some similar proteins from the PDB
fetch 1oky 1h1w 1okz 1uu3 1uu7 1uu8 1uu9 1uvr, async=0
# align them all to 1oky; their ligands
# should all now be aligned
alignto 1oky
# highlight the ligands
as sticks, org
# select one of the atoms in the organic small mol
sele /1uu3//A/LY4`1374/NAT
# select entire molecules very near the chosen atom
select bm. all within 1 of (sele)
# remove the proteins; just look at small molecules
remove not (sele)
# create maps for all the ligands
python
for x in cmd.get_names():
cmd.map_new( "map_" + x, "gaussian", 0.5, x)
python end
# calculate the average map
map_set avgMap, average, map*
# show as transparent surface
set transparency, 0.5
isosurface avgSurface, avgMap, 1.0
orient vis