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James.watney: /* Examples */

2011-02-10T18:38:08Z

Examples

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[[Image:Map_set_ex.png‎|right|thumb|300px|Map_set created this consensus volume representation of aligned ligands bound to kinases. See example below.]]
[[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 =
<source lang="python">
map_set name, operator, operands, target_state, source_state
</source>
operator may be,
* average
* copy
* difference
* maximum
* minimum
* sum
* unique

= Examples =
<source lang="python">
# add 3 maps
map_set my_sum, sum, map1 map2 map3

# calculate the average map
map_set my_avg, average, map1 map2 map3

</source>

= Detailed Example =
This example shows you how to create a consensus map of the bound ligand in a conserved pocket.

<source lang="python">
# 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
</source>

= Notes =
source_state = 0 means all states

target_state = -1 means current state

This is an experimental function.

= See Also =
[[Map_new]]

[[Category:Commands]]

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