Map set: Difference between revisions

From PyMOLWiki
Jump to navigation Jump to search
(Created page with "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 ma...")
 
No edit summary
Line 6: Line 6:
</source>
</source>
operator may be,
operator may be,
* average  
* average  
* copy
* copy
* difference  
* difference  
* maximum
* maximum
* minimum
* minimum
* sum   
* sum   
* unique     
* unique     
   
   
= Examples =
= Examples =
Line 23: Line 23:


</source>     
</source>     
NOTES
    source_state = 0 means all states
    target_state = -1 means current state
   
    experimental
   


= Detailed Example =
= Detailed Example =
Line 72: Line 63:
orient vis
orient vis
</source>
</source>
= Notes =
source_state = 0 means all states
target_state = -1 means current state
   
This is an experimental function.   


= See Also =
= See Also =

Revision as of 16:05, 8 February 2011

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

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

Notes

source_state = 0 means all states

target_state = -1 means current state

This is an experimental function.


See Also

Map_new