Editing Ramp New (section)

==== 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>