Ramp New

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ramp_new creates a color ramp based on a map potential value or based on proximity to a molecular object.

Color ramps are extremely powerful but complicated to use.

In the simplest case, they can be used to color representations based on the potential values found in a map object at the corresponding positions in space. In another simple case, representations can be colored based on proximity to a target. Note that since ramp targets must themselves be real objects (not merely selections), the "create" command may be needed in order to generate an appropriate target. In more complicated cases, they can be used to color representations on one object based atoms found in another. Ramps can operate recursively. In other words, the output color from one ramp can be used as the input color for another. For example, you could color by map potential within a certain distance of the target object, beyond which, a uniform color is applied.


Contents

Usage

 
# normal PyMOL usage
ramp_new name, map_name [, range [, color [, state [, selection [,
        beyond [, within [, sigma [, zero ]]]]]]]]
 
 
# in the API
cmd.ramp_new(string name, string map_name, list range, list color, 
  int state, string selection, float beyond, float
  within, float sigma, int zero, int quiet)

Examples

Simple Example

ramp_new e_pot_color, e_pot_map, [-10, 0, 10], [red, white, blue]

This creates a new ramp object named e_pot_color, based on the values of the potential found in e_pot_map.

Elaborate examples

Ramp + Distance Measure

Using a ramp and a distance measure, we can color the surface by some property--here, I'll chose distance from some important atom in the receptor to the ligand atom.

To reproduce the results shown here you must do the following:


Another possible application of the ramp_new command can be the representation of the ELF function [1]. This function can be calculated with the TopMod software [2].

isosurface elf, H2O_elf, 0.8
ramp_new ramp, H2O_esyn, [1, 2, 3, 5], [tv_orange, lightblue, palegreen, deeppurple]
set surface_color, ramp, elf
rebuild

Surface Colored by Distance from a Point

See Spectrum for another method that allows for more flexible coloring schemes, but needs more work to get there.

This example shows how to color a protein surface by its distance from a given point:

# fetch a friendly protein
 
fetch 1hug, async=0
 
# show it as a surface
 
as surface
 
# create a pseudoatom at the origin; we will
# measure the distance from this point
 
pseudoatom pOrig, pos=(0,0,0), label=origin
 
# create a new color ramp, measuring the distance
# from pOrig to 1hug, colored as rainbow
 
ramp_new proximityRamp, pOrig, selection=1hug, range=[5,65], color=rainbow
 
# set the surface color to the ramp coloring
 
set surface_color, proximityRamp, 1hug
 
# some older PyMOLs need this recoloring/rebuilding
 
recolor; rebuild

Coloring a Viral Capsid by Distance from Core

# create a pseudoatom at the origin-- we will
# measure the distance from this point
 
pseudoatom pOrig, pos=(0,0,0), label=origin
 
# fetch and build the capsid
 
fetch 2xpj, async=0, type=pdb1
split_states 2xpj
delete 2xpj
 
# show all 60 subunits it as a surface
# this will take a few minutes to calculate
 
as surface
 
# create a new color ramp, measuring the distance
# from pOrig to 1hug, colored as rainbow
 
ramp_new proximityRamp, pOrig, selection=(2xpj*), range=[110,160], color=rainbow
 
# set the surface color to the ramp coloring
 
set surface_color, proximityRamp, (2xpj*)
 
# some older PyMOLs need this recoloring/rebuilding
 
recolor

See Also

load, color, create, slice, gradient, Expand_To_Surface

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