slice_new name, map, [state, [source_state]]
slice name, map, [state, [source_state]]
- 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)
# 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.
cmd.slice_new(string slice_name, string map_name, integer state=0, integer source_state=0)
Mis-identified as "slice_map" in documentation. slice or 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).
- PyMOL Source code