PyMOL Wiki - User contributions [en]

User:DBorhani

2011-03-17T03:14:07Z

DBorhani:

David W. Borhani 
----
D. E. Shaw Research 
120 West Forty-Fifth Street, 39th Floor 
New York, NY 10036 
[mailto:David.Borhani@DEShawResearch.com David.Borhani@DEShawResearch.com] 
212-478-0698 
[http://www.deshawresearch.com D. E. Shaw Research]

Slice new

2011-03-17T03:12:03Z

DBorhani:

#REDIRECT [[slice]]
{{DISPLAYTITLE:Slice_new}}

[[Category:Commands|Slice_new]]
[[Category:States|Slice_new]]
[[Category:Electron_Density]]
[[Category:Maps]]

Slice new

2011-03-17T03:05:56Z

DBorhani:

#REDIRECT [[slice]]
{{PAGENAME:Slice_new}

[[Category:Commands|Slice]]
[[Category:States|Slice]]
[[Category:Electron_Density]]
[[Category:Maps]]

Slice new

2011-03-16T21:55:39Z

DBorhani:

#REDIRECT [[slice]]

[[Category:Commands|Slice]]
[[Category:States|Slice]]
[[Category:Electron_Density]]
[[Category:Maps]]

Slice new

2011-03-16T21:54:01Z

DBorhani: Redirected page to Slice

#REDIRECT [[slice]]

Slice

2011-03-16T21:49:51Z

DBorhani:

[[File:Slice_example_2_screenshot.png|600px|thumb|right|border|Screenshot of slice example #2]]

[[slice]] creates a slice object from a [[:Category:Maps|map]] object.

== USAGE ==
<source lang="python">
slice_new name, map, [state, [source_state]]
</source>

''or''

<source lang="python">
slice name, map, [state, [source_state]]
</source>

== ARGUMENTS ==
*'''name''' = the name for the new slice object (string)
*'''map''' = the name of the map object to use for computing the slice (string)
*'''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 ==
<source lang="python">
# 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
# (Optional: Adjust view direction to your liking)
# Create a map slice *perpendicular* to the current view.
# The slice seems to be in the center of the APBS (or other) volmap. Map "tracking" is off 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

# Adjust the fineness of the slice color gradations:
cmd.set('slice_grid',0.1) # normally at 0.3; much finer than 0.05 gets a bit slow

# Map slices can be moved, relative to other fixed objects (e.g., your protein/DNA/RNA),
# by turning tracking on (Action menu), and the using the Shift-MouseWheel to move
# the slice forward in and backward in Z. Adjust fineness of this Z-motion with:
# cmd.set('mouse_wheel_scale',0.05) # normally at 0.5

# The result is shown in the image above.
</source>

== PYMOL API ==
<source lang="python">
cmd.slice_new(string slice_name, string map_name, integer state=0, integer source_state=0)
</source>

== NOTES ==
Mis-identified as "slice_map" in documentation. [[slice]] or [[slice|slice_new]] is the correct command. Documentation also mentions two optional parameters which seem to be no longer supported (opacity = opacity of the new slice, and resolution = the number of pixels per sampling).

== SEE ALSO ==
[[isomesh]], [[isodot]], [[load]]

== References ==
* PyMOL Source code

[[Category:Commands|Slice]]
[[Category:States|Slice]]
[[Category:Electron_Density]]
[[Category:Maps]]

Slice

2011-03-16T21:49:20Z

DBorhani:

[[File:Slice_example_2_screenshot.png|500px|thumb|right|border|Screenshot of slice example #2]]

[[slice]] creates a slice object from a [[:Category:Maps|map]] object.

== USAGE ==
<source lang="python">
slice_new name, map, [state, [source_state]]
</source>

''or''

<source lang="python">
slice name, map, [state, [source_state]]
</source>

== ARGUMENTS ==
*'''name''' = the name for the new slice object (string)
*'''map''' = the name of the map object to use for computing the slice (string)
*'''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 ==
<source lang="python">
# 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
# (Optional: Adjust view direction to your liking)
# Create a map slice *perpendicular* to the current view.
# The slice seems to be in the center of the APBS (or other) volmap. Map "tracking" is off 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

# Adjust the fineness of the slice color gradations:
cmd.set('slice_grid',0.1) # normally at 0.3; much finer than 0.05 gets a bit slow

# Map slices can be moved, relative to other fixed objects (e.g., your protein/DNA/RNA),
# by turning tracking on (Action menu), and the using the Shift-MouseWheel to move
# the slice forward in and backward in Z. Adjust fineness of this Z-motion with:
# cmd.set('mouse_wheel_scale',0.05) # normally at 0.5

# The result is shown in the image above.
</source>

== PYMOL API ==
<source lang="python">
cmd.slice_new(string slice_name, string map_name, integer state=0, integer source_state=0)
</source>

== NOTES ==
Mis-identified as "slice_map" in documentation. [[slice]] or [[slice|slice_new]] is the correct command. Documentation also mentions two optional parameters which seem to be no longer supported (opacity = opacity of the new slice, and resolution = the number of pixels per sampling).

== SEE ALSO ==
[[isomesh]], [[isodot]], [[load]]

== References ==
* PyMOL Source code

[[Category:Commands|Slice]]
[[Category:States|Slice]]
[[Category:Electron_Density]]
[[Category:Maps]]

Slice

2011-03-16T21:48:49Z

DBorhani:

[[File:Slice_example_2_screenshot.png|600px|thumb|center|border|Screenshot of slice example #2]]

[[slice]] creates a slice object from a [[:Category:Maps|map]] object.

== USAGE ==
<source lang="python">
slice_new name, map, [state, [source_state]]
</source>

''or''

<source lang="python">
slice name, map, [state, [source_state]]
</source>

== ARGUMENTS ==
*'''name''' = the name for the new slice object (string)
*'''map''' = the name of the map object to use for computing the slice (string)
*'''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 ==
<source lang="python">
# 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
# (Optional: Adjust view direction to your liking)
# Create a map slice *perpendicular* to the current view.
# The slice seems to be in the center of the APBS (or other) volmap. Map "tracking" is off 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

# Adjust the fineness of the slice color gradations:
cmd.set('slice_grid',0.1) # normally at 0.3; much finer than 0.05 gets a bit slow

# Map slices can be moved, relative to other fixed objects (e.g., your protein/DNA/RNA),
# by turning tracking on (Action menu), and the using the Shift-MouseWheel to move
# the slice forward in and backward in Z. Adjust fineness of this Z-motion with:
# cmd.set('mouse_wheel_scale',0.05) # normally at 0.5

# The result is shown in the image above.
</source>

== PYMOL API ==
<source lang="python">
cmd.slice_new(string slice_name, string map_name, integer state=0, integer source_state=0)
</source>

== NOTES ==
Mis-identified as "slice_map" in documentation. [[slice]] or [[slice|slice_new]] is the correct command. Documentation also mentions two optional parameters which seem to be no longer supported (opacity = opacity of the new slice, and resolution = the number of pixels per sampling).

== SEE ALSO ==
[[isomesh]], [[isodot]], [[load]]

== References ==
* PyMOL Source code

[[Category:Commands|Slice]]
[[Category:States|Slice]]
[[Category:Electron_Density]]
[[Category:Maps]]

Slice

2011-03-16T21:47:50Z

DBorhani:

[[slice]] creates a slice object from a [[:Category:Maps|map]] object.

[[File:Slice_example_2_screenshot.png|400px|thumb|right|border|Screenshot of slice example #2]]

== USAGE ==
<source lang="python">
slice_new name, map, [state, [source_state]]
</source>

''or''

<source lang="python">
slice name, map, [state, [source_state]]
</source>

== ARGUMENTS ==
*'''name''' = the name for the new slice object (string)
*'''map''' = the name of the map object to use for computing the slice (string)
*'''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 ==
<source lang="python">
# 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
# (Optional: Adjust view direction to your liking)
# Create a map slice *perpendicular* to the current view.
# The slice seems to be in the center of the APBS (or other) volmap. Map "tracking" is off 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

# Adjust the fineness of the slice color gradations:
cmd.set('slice_grid',0.1) # normally at 0.3; much finer than 0.05 gets a bit slow

# Map slices can be moved, relative to other fixed objects (e.g., your protein/DNA/RNA),
# by turning tracking on (Action menu), and the using the Shift-MouseWheel to move
# the slice forward in and backward in Z. Adjust fineness of this Z-motion with:
# cmd.set('mouse_wheel_scale',0.05) # normally at 0.5

# The result is shown in the image above.
</source>

== PYMOL API ==
<source lang="python">
cmd.slice_new(string slice_name, string map_name, integer state=0, integer source_state=0)
</source>

== NOTES ==
Mis-identified as "slice_map" in documentation. [[slice]] or [[slice|slice_new]] is the correct command. Documentation also mentions two optional parameters which seem to be no longer supported (opacity = opacity of the new slice, and resolution = the number of pixels per sampling).

== SEE ALSO ==
[[isomesh]], [[isodot]], [[load]]

== References ==
* PyMOL Source code

[[Category:Commands|Slice]]
[[Category:States|Slice]]
[[Category:Electron_Density]]
[[Category:Maps]]

Slice

2011-03-16T21:46:37Z

DBorhani:

[[slice]] creates a slice object from a [[:Category:Maps|map]] object.

[[File:Slice_example_2_screenshot.png|400px|thumb|left|border|Screenshot of slice example #2]]

== USAGE ==
<source lang="python">
slice_new name, map, [state, [source_state]]
</source>

''or''

<source lang="python">
slice name, map, [state, [source_state]]
</source>

== ARGUMENTS ==
*'''name''' = the name for the new slice object (string)
*'''map''' = the name of the map object to use for computing the slice (string)
*'''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 ==
<source lang="python">
# 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
# (Optional: Adjust view direction to your liking)
# Create a map slice *perpendicular* to the current view.
# The slice seems to be in the center of the APBS (or other) volmap. Map "tracking" is off 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

# Adjust the fineness of the slice color gradations:
cmd.set('slice_grid',0.1) # normally at 0.3; much finer than 0.05 gets a bit slow

# Map slices can be moved, relative to other fixed objects (e.g., your protein/DNA/RNA),
# by turning tracking on (Action menu), and the using the Shift-MouseWheel to move
# the slice forward in and backward in Z. Adjust fineness of this Z-motion with:
# cmd.set('mouse_wheel_scale',0.05) # normally at 0.5

# The result is shown in the image above.
</source>

== PYMOL API ==
<source lang="python">
cmd.slice_new(string slice_name, string map_name, integer opacity=1, integer resolution=5, integer state=0, integer source_state=0)
</source>

== NOTES ==
Mis-identified as "slice_map" in documentation. [[slice]] or [[slice|slice_new]] is the correct command. Documentation also mentions two optional parameters which seem to be no longer supported (opacity = opacity of the new slice, and resolution = the number of pixels per sampling).

== SEE ALSO ==
[[isomesh]], [[isodot]], [[load]]

== References ==
* PyMOL Source code

[[Category:Commands|Slice]]
[[Category:States|Slice]]
[[Category:Electron_Density]]
[[Category:Maps]]

Slice

2011-03-16T21:45:37Z

DBorhani:

[[slice]] creates a slice object from a [[:Category:Maps|map]] object.

== USAGE ==
<source lang="python">
slice_new name, map, [state, [source_state]]
</source>

''or''

<source lang="python">
slice name, map, [state, [source_state]]
</source>

== ARGUMENTS ==
*'''name''' = the name for the new slice object (string)
*'''map''' = the name of the map object to use for computing the slice (string)
*'''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)

[[File:Slice_example_2_screenshot.png|200px|thumb|left|border|Screenshot of slice example #2]]
 

== EXAMPLES ==
<source lang="python">
# 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
# (Optional: Adjust view direction to your liking)
# Create a map slice *perpendicular* to the current view.
# The slice seems to be in the center of the APBS (or other) volmap. Map "tracking" is off 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

# Adjust the fineness of the slice color gradations:
cmd.set('slice_grid',0.1) # normally at 0.3; much finer than 0.05 gets a bit slow

# Map slices can be moved, relative to other fixed objects (e.g., your protein/DNA/RNA),
# by turning tracking on (Action menu), and the using the Shift-MouseWheel to move
# the slice forward in and backward in Z. Adjust fineness of this Z-motion with:
# cmd.set('mouse_wheel_scale',0.05) # normally at 0.5

# The result is shown in the image above.
</source>

== PYMOL API ==
<source lang="python">
cmd.slice_new(string slice_name, string map_name, integer opacity=1, integer resolution=5, integer state=0, integer source_state=0)
</source>

== NOTES ==
Mis-identified as "slice_map" in documentation. [[slice]] or [[slice|slice_new]] is the correct command. Documentation also mentions two optional parameters which seem to be no longer supported (opacity = opacity of the new slice, and resolution = the number of pixels per sampling).

== SEE ALSO ==
[[isomesh]], [[isodot]], [[load]]

== References ==
* PyMOL Source code

[[Category:Commands|Slice]]
[[Category:States|Slice]]
[[Category:Electron_Density]]
[[Category:Maps]]

Slice

2011-03-16T18:01:03Z

DBorhani:

[[slice]] creates a slice object from a [[:Category:Maps|map]] object.

== USAGE ==
<source lang="python">
slice_new name, map, [opacity, [resolution, [state, [source_state]]]]
</source>

''or''

<source lang="python">
slice name, map, [opacity, [resolution, [state, [source_state]]]]
</source>

== 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 ==
<source lang="python">
# 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:
</source>
[[File:Slice_example_2_screenshot.png|200px|thumb|left|border|Screenshot of slice example #2]]
 

== PYMOL API ==
<source lang="python">
cmd.slice_new(string slice_name, string map_name, integer opacity=1, integer resolution=5, integer state=0, integer source_state=0)
</source>

== NOTES ==
Occasionally mis-identified as "slice_map" in documentation. [[slice]] or [[slice|slice_new]] is the correct command.

== SEE ALSO ==
[[isomesh]], [[isodot]], [[load]]

== References ==
* PyMOL Source code

[[Category:Commands|Slice]]
[[Category:States|Slice]]
[[Category:Electron_Density]]
[[Category:Maps]]

Slice

2011-03-16T17:57:57Z

DBorhani:

[[slice]] creates a slice object from a [[:Category:Maps|map]] object.

== USAGE ==
<source lang="python">
slice_new name, map, [opacity, [resolution, [state, [source_state]]]]
</source>

''or''

<source lang="python">
slice name, map, [opacity, [resolution, [state, [source_state]]]]
</source>

== 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 ==
<source lang="python">
# 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:
</source>
[[File:Slice_example_2_screenshot.png|200px|thumb|left|Screenshot of slice example #2]]

== PYMOL API ==
<source lang="python">
cmd.slice_new(string slice_name, string map_name, integer opacity=1, integer resolution=5, integer state=0, integer source_state=0)
</source>

== NOTES ==
Occasionally mis-identified as "slice_map" in documentation. [[slice]] or [[slice|slice_new]] is the correct command.

== SEE ALSO ==
[[isomesh]], [[isodot]], [[load]]

== References ==
* PyMOL Source code

[[Category:Commands|Slice]]
[[Category:States|Slice]]
[[Category:Electron_Density]]
[[Category:Maps]]

Slice

2011-03-16T17:55:18Z

DBorhani:

[[slice]] creates a slice object from a [[:Category:Maps|map]] object.

== USAGE ==
<source lang="python">
slice_new name, map, [opacity, [resolution, [state, [source_state]]]]
</source>

''or''

<source lang="python">
slice name, map, [opacity, [resolution, [state, [source_state]]]]
</source>

== 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 ==
<source lang="python">
# 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:Slice_example_2.png]]
</source>

== PYMOL API ==
<source lang="python">
cmd.slice_new(string slice_name, string map_name, integer opacity=1, integer resolution=5, integer state=0, integer source_state=0)
</source>

== NOTES ==
Occasionally mis-identified as "slice_map" in documentation. [[slice]] or [[slice|slice_new]] is the correct command.

== SEE ALSO ==
[[isomesh]], [[isodot]], [[load]]

== References ==
* PyMOL Source code

[[Category:Commands|Slice]]
[[Category:States|Slice]]
[[Category:Electron_Density]]
[[Category:Maps]]

File:Slice example 2.png

2011-03-16T17:54:14Z

DBorhani: Slice example #2

Slice example #2

File:Slice example 2 screenshot.png

2011-03-16T17:53:29Z

DBorhani: Pymol screen shot of slice example #2

Pymol screen shot of slice example #2

Slice

2011-03-16T17:43:39Z

DBorhani:

[[slice]] creates a slice object from a [[:Category:Maps|map]] object.

== USAGE ==
<source lang="python">
slice_new name, map, [opacity, [resolution, [state, [source_state]]]]
</source>

''or''

<source lang="python">
slice name, map, [opacity, [resolution, [state, [source_state]]]]
</source>

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

== PYMOL API ==
<source lang="python">
cmd.slice_new(string slice_name, string map_name, integer opacity=1, integer resolution=5, integer state=0, integer source_state=0)
</source>

== NOTES ==
Occasionally mis-identified as "slice_map" in documentation. [[slice]] or [[slice|slice_new]] is the correct command.

== SEE ALSO ==
[[isomesh]], [[isodot]], [[load]]

== References ==
* PyMOL Source code

[[Category:Commands|Slice]]
[[Category:States|Slice]]
[[Category:Electron_Density]]
[[Category:Maps]]

Slice

2011-03-16T17:37:22Z

DBorhani:

Slice

2011-03-16T17:33:36Z

DBorhani:

Slice

2011-03-16T17:29:07Z

DBorhani:

Slice

2011-03-16T17:27:47Z

DBorhani:

Slice

2011-03-16T17:06:33Z

DBorhani: Created page with "slice creates a slice object from a map object representations. == USAGE == <source lang="python"> slice name, map, [opacity, [resolution, [sta..."

[[slice]] creates a slice object from a map object [[:Category:Representations|representations]].

== USAGE ==
<source lang="python">
slice name, map, [opacity, [resolution, [state, [source_state]]]]
</source>

== 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)
*'''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 ==
<source lang="python">
# show the backbone as lines
show_as lines, name ca or name c or name n

# show everything as a ribbon
show_as ribbon
</source>
== PYMOL API ==
<source lang="python">
cmd.show_as(string representation, string selection)
</source>

== NOTES ==
Often mis-identified as "slice_map" in the help. [[slice] is the correct command.

== SEE ALSO ==
[[isomesh]], [[isodot]], [[load]]

== References ==
* PyMOL Source code

[[Category:Commands|Slice]]
[[Category:View Module|Slice]]

User:DBorhani

2011-03-16T16:49:11Z

DBorhani:

David Borhani 
----
D. E. Shaw Research 
120 West Forty-Fifth Street, 39th Floor 
New York, NY 10036 
[mailto:David.Borhani@DEShawResearch.com David.Borhani@DEShawResearch.com] 
212-478-0698 
[http://www.deshawresearch.com D. E. Shaw Research]

User:DBorhani

2011-03-16T16:47:29Z

DBorhani:

David Borhani 
----
D. E. Shaw Research 
120 West Forty-Fifth Street, 39th Floor 
New York, NY 10036 
[mail_to:David.Borhani@DEShawResearch.com David.Borhani@DEShawResearch.com] 
212-478-0698 
[http://www.deshawresearch.com D. E. Shaw Research]

User:DBorhani

2011-03-16T16:40:58Z

DBorhani:

David Borhani
----
D. E. Shaw Research
120 West Forty-Fifth Street, 39th Floor
New York, NY 10036
David.Borhani@DEShawResearch.com
212-478-0698
http://www.deshawresearch.com

User:DBorhani

2011-03-16T16:39:36Z

DBorhani: Created page with "David Borhani ---- D. E. Shaw Research 120 West Forty-Fifth Street, 39th Floor New York, NY 10036 [mail_to:David.Borhani@DEShawResearch.com] 212-478-0698 [http://www.deshawresear..."

David Borhani
----
D. E. Shaw Research
120 West Forty-Fifth Street, 39th Floor
New York, NY 10036
[mail_to:David.Borhani@DEShawResearch.com]
212-478-0698
[http://www.deshawresearch.com]