Editing Ramp New (section)

== Examples ==

=== Color surface by an APBS calculated electrostatic map ===

Example map: http://pymol.org/tmp/1ubq_apbs.dx

<source lang="python">
load 1ubq_apbs.dx, e_pot_map
fetch 1ubq, async=0
as surface

ramp_new e_pot_color, e_pot_map, [-5, 0, 5], [red, white, blue]
set surface_color, e_pot_color
set surface_ramp_above_mode
</source>

=== Color binding pocket by proximity to ligand ===

* Ligand: blue
* Protein within 4 Angstrom of ligand: red
* Protein beyond 8 Angstrom of ligand: yellow

<source lang="python">
fetch 1rx1, async=0
extract ligand, organic
color blue, ligand
show surface

ramp_new prox, ligand, [4, 8], [red, yellow]
color prox, 1rx1
</source>

=== Color isosurface by closest atom ===

''See also the [[huge surfaces]] example.''

Color the isosurface within 2 Angstrom of the protein (without solvent) by atom colors. Everything beyond 2 Angstrom will be gray.

<source lang="python">
fetch 1rx1, map, async=0, type=2fofc
isosurface surf, map

fetch 1rx1, mol, async=0
remove solvent

ramp_new prox, mol, [0, 2, 2], [atomic, atomic, gray]
color prox, surf
</source>

Updating the atom colors is possible, for example:

<source lang="python">
spectrum
recolor
</source>

=== More user provided 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.

<gallery perrow=3 widths=250 heights=250>
Image:Surface_by_prop3.png|Ligand surface colored by distance from some given atom.  The remainder of the protein is hidden to more clearly visualize the calculated distances and surface color
Image:Surface_by_prop.png
</gallery>

To reproduce the results shown here you must do the following:
* obtain a protein
* calculate some property for some set of atoms (like distance from some central location) and stuff the values into the b-factor
* create a new object from the atoms for which you just measured a property
* create a new ramp from the object with ramp_new
* set the surface color of the new object


Another possible application of the ramp_new command can be the representation of the ELF function [http://en.wikipedia.org/wiki/Electron_localization_function]. This function can be calculated with the TopMod software [http://www.lct.jussieu.fr/suite64.html].

* Load the cube file containing the ELF function, e.g. H2O_elf.cube.
* Create an isosurface with a contour level of 0.8.
<source lang="python">isosurface elf, H2O_elf, 0.8</source>
* Load the cube containing the basin information, e.g. H20_esyn.cube. Basically in this cube for each point in the first cube you have either one of the numbers from 1 to 5. More details on what these numbers mean can be found in the TopMod manual.
* Create a new ramp.
<source lang="python">ramp_new ramp, H2O_esyn, [1, 2, 3, 5], [tv_orange, lightblue, palegreen, deeppurple]</source>
* Assign the color ramp to the ELF isosurface.
<source lang="python">set surface_color, ramp, elf</source>
* Rebuild if necessary.
<source lang="python">rebuild</source>

<gallery perrow=2 widths=250 heights=250>
Image:H2O.png|Localization domains of H2O. The bounding isosurface is ELF=0.8
Image:BeCl2.png|Localization domains of BeCl2. The bounding isosurface is ELF=0.8
</gallery>

==== 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.

<gallery widths=400 heights=250>
Image:Measure.png
</gallery>

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

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

====Coloring a Viral Capsid by Distance from Core====
<gallery heights=350 widths=350>
Image:Capsid_by_dist.png
</gallery>
<source lang="python">
# 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
</source>