Difference between revisions of "Slice"

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<source lang="python">  
 
<source lang="python">  
 
# Create a map slice plane perpendicular to current view
 
# Create a map slice plane perpendicular to current view
slice_new my_new_slice_1, my_map
+
slice a_new_slice, a_map
 +
 
 +
 
 +
# A more complicated example that shows how to create multiple slices
 +
# (in this case, 3 slices perpendicular to each other), each colored
 +
# with a different color ramp and different contour levels:
 +
 
 +
# Reset the view, to align view on XYZ axes
 +
reset
 +
# Create a map slice perpendicular to current view. (Non-tracking by default.)
 +
slice slice_A, apbs_map
 +
# Rotate camera 90 degrees about the vertical axis
 +
turn y, 90
 +
# Second, perpendicular, slice
 +
slice slice_B, apbs_map
 +
# Rotate again, this time about the horizontal
 +
turn x, 90
 +
# Third slice
 +
slice slice_C, apbs_map
 +
 
 +
# Define new color ramps: ramp_name, map_object, list of low/mid/hi values, 3 RGB triplets
 +
ramp_new ramp1010RWB, apbs_map, [-10,0,10], [ [1,0,0], [1,1,1], [0,0,1] ]
 +
ramp_new ramp11RYG, apbs_map, [-1,0,1], [ [1,0,0], [1,1,0], [0,1,0] ]
 +
ramp_new ramp55MltGO, apbs_map, [-5,0,5], [ [0,1,1], [0.5,1,0.5], [1,0.5,0.2] ]
 +
 
 +
# Color the map slices
 +
color ramp1010RWB, slice_A
 +
color ramp11RYG, slice_B
 +
color ramp55MltGO, slice_C
 +
 
 +
# The result:
 +
[[File:Example.jpg]]
 
</source>  
 
</source>  
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 +
  
 
== PYMOL API ==
 
== PYMOL API ==
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== NOTES ==
 
== NOTES ==
Occasionally mis-identified as "slice_map" in documentation. [[Category:Commands|Slice]] or [[Category:Commands|Slice_new]] is the correct command.
+
Occasionally mis-identified as "slice_map" in documentation. [[slice]] or [[slice|slice_new]] is the correct command.
 
   
 
   
 
== SEE ALSO ==
 
== SEE ALSO ==

Revision as of 12:43, 16 March 2011

slice creates a slice object from a map object.

USAGE

slice_new name, map, [opacity, [resolution, [state, [source_state]]]]

or

slice name, map, [opacity, [resolution, [state, [source_state]]]]

ARGUMENTS

  • name = the name for the new slice object (string)
  • map = the name of the map object to use for computing the slice (string)
  • opacity = opacity of the new slice (default=1 [opaque])
  • resolution = the number of pixels per sampling (default=5)
  • state = the state into which the object should be loaded (default=1; set state=0 to append new mesh as a new state)
  • source_state = the state of the map from which the object should be loaded (default=0)

EXAMPLES

 
# Create a map slice plane perpendicular to current view
slice a_new_slice, a_map


# A more complicated example that shows how to create multiple slices
# (in this case, 3 slices perpendicular to each other), each colored
# with a different color ramp and different contour levels:

# Reset the view, to align view on XYZ axes
reset
# Create a map slice perpendicular to current view. (Non-tracking by default.)
slice slice_A, apbs_map
# Rotate camera 90 degrees about the vertical axis
turn y, 90
# Second, perpendicular, slice
slice slice_B, apbs_map
# Rotate again, this time about the horizontal
turn x, 90
# Third slice
slice slice_C, apbs_map

# Define new color ramps: ramp_name, map_object, list of low/mid/hi values, 3 RGB triplets
ramp_new ramp1010RWB, apbs_map, [-10,0,10], [ [1,0,0], [1,1,1], [0,0,1] ]
ramp_new ramp11RYG, apbs_map, [-1,0,1], [ [1,0,0], [1,1,0], [0,1,0] ]
ramp_new ramp55MltGO, apbs_map, [-5,0,5], [ [0,1,1], [0.5,1,0.5], [1,0.5,0.2] ]

# Color the map slices
color ramp1010RWB, slice_A
color ramp11RYG, slice_B
color ramp55MltGO, slice_C

# The result:
[[File:Example.jpg]]


PYMOL API

 
cmd.slice_new(string slice_name, string map_name, integer opacity=1, integer resolution=5, integer state=0, integer source_state=0)

NOTES

Occasionally mis-identified as "slice_map" in documentation. slice or slice_new is the correct command.

SEE ALSO

isomesh, isodot, load

References

  • PyMOL Source code