Ramp New - Revision history

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second example didn't work in 1.7.6

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2014-03-28T03:08:55Z

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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.

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

*'''ramp_name''' = string: name of the ramp object
*'''map_name''' = string: name of the map (for potential) or molecular object (for proximity)
*'''range''' = list: values corresponding to slots in the ramp
*'''color''' = list: colors corresponding to slots in the ramp or a given palette name: afmhot, grayscale, object, rainbow, traditional, grayable, hot, ocean, and sludge
*'''state''' = integer: state identifier
*'''selection''' = selection: for automatic ranging
*'''beyond''' = number: with automatic ranging, are we excluding values beyond a certain distance from the selection?
*'''within''' = number: with automatic ranging, are we only including valuess within a certain distance from the selection?
*'''sigma''' = number: with automatic ranging, how many standard deviations from the mean do we go?
*'''zero''' = integer: with automatic ranging, do we force the central value to be zero?

= Examples =
== Simple Example ==
<source lang="python">
ramp_new e_pot_color, e_pot_map, [-10, 0, 10], [red, white, blue]
</source>
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.

<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_prop2.png
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>

= See Also =
[[load]], [[color]], [[create]], [[slice]], [[gradient]], [[Expand_To_Surface]]

[[Category:Commands|Ramp new]]
[[Category:Coloring]]

Mretegan at 22:17, 4 July 2010

2010-07-04T22:17:33Z

Mretegan at 22:16, 4 July 2010

2010-07-04T22:16:44Z

Mretegan: Restructuring and addtions.

2010-07-04T22:14:55Z

Restructuring and addtions.

Mretegan at 21:20, 4 July 2010

2010-07-04T21:20:57Z

New page

Vinnyrose: moved Ramp new to Ramp New

2009-06-20T14:35:46Z

moved Ramp new to Ramp New

Vinnyrose at 13:36, 20 June 2009

2009-06-20T13:36:20Z

New page

= Overview =
[[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.

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

*'''name''' = string: name of the ramp object
*'''map_name''' = string: name of the map (for potential) or molecular object (for proximity)
*'''range''' = list: values corresponding to slots in the ramp
*'''color''' = list: colors corresponding to slots in the ramp
*'''state''' = integer: state identifier
*'''selection''' = selection: for automatic ranging
*'''beyond''' = number: with automatic ranging, are we excluding values beyond a certain distance from the selection?
*'''within''' = number: with automatic ranging, are we only including valuess within a certain distance from the selection?
*'''sigma''' = number: with automatic ranging, how many standard deviations from the mean do we go?
*'''zero''' = integer: with automatic ranging, do we force the central value to be zero?

= Example =
== Simple Example ==
<source lang="python">
ramp_new e_pot_color, e_pot_map, [-10,0,10], [red,white,blue]
</source>

== Normal Usage ==
<source lang="python">
load pdbset1.pqr
load pdbset_1.dx

load pdbset3.pqr
load pdbset_3.dx

ramp_new ramp1, pdbset_1, [ -3, 0, 3]
ramp_new ramp3, pdbset_3, [ -3, 0, 3]

show surface

set surface_ramp_above_mode

set surface_color, ramp1, pdbset1
set surface_color, ramp3, pdbset3
</source>

= See Also =
[[load]], [[color]], [[create]], [[slice]], [[gradient]]

[[Category:Commands|Ramp new]]

@@ Line 67: / Line 67: @@
 extract ligand, organic
 color blue, ligand
-as sticks
+show surface
 ramp_new prox, ligand, [4, 8], [red, yellow]

← Older revision	Revision as of 17:32, 14 August 2015
(No difference)

@@ Line 77: / Line 77: @@
 * Assign the color ramp to the ELF isosurface.
 <source lang="python">set surface_color, ramp, elf</source>
-* Rebuild is necessary.
+* Rebuild if necessary.
 <source lang="python">rebuild</source>

@@ Line 69: / Line 69: @@
 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
+* Load the cube file containing the ELF function, e.g. H2O_elf.cube.
-* Create an isosurface with a contour level of 0.8
+* 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
+* Assign the color ramp to the ELF isosurface.
 <source lang="python">set surface_color, ramp, elf</source>
-* Rebuild
+* Rebuild is necessary.
 <source lang="python">rebuild</source>
 <gallery perrow=2 widths=250 heights=250>
-Image:H2O.png|Localization domains of H2O. The bounding isosurfaces are ELF=0.8
+Image:H2O.png|Localization domains of H2O. The bounding isosurface is ELF=0.8
-Image:BeCl2.png|Localization domains of BeCl2. The bounding isosurfaces are ELF=0.8
+Image:BeCl2.png|Localization domains of BeCl2. The bounding isosurface is ELF=0.8
 </gallery>

@@ Line 4: / Line 4: @@
 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.
@@ Line 36: / Line 20: @@
 </source>
-*'''name''' = string: name of the ramp object
+*'''ramp_name''' = string: name of the ramp object
 *'''map_name''' = string: name of the map (for potential) or molecular object (for proximity)
 *'''range''' = list: values corresponding to slots in the ramp
@@ Line 46: / Line 30: @@
 *'''sigma''' = number: with automatic ranging, how many standard deviations from the mean do we go?
 *'''zero''' = integer: with automatic ranging, do we force the central value to be zero?
-−
-= Example =
+= Examples =
 == Simple Example ==
 <source lang="python">
-ramp_new e_pot_color, e_pot_map, [-10,0,10], [red,white,blue]
+ramp_new e_pot_color, e_pot_map, [-10, 0, 10], [red, white, blue]
 </source>
-== Normal Usage ==
+To reproduce the results shown here you must do the following:
-<source lang="python">
+* obtain a protein
-load pdbset1.pqr
+* calculate some property for some set of atoms (like distance from some central location) and stuff the values into the b-factor
-load pdbset_1.dx
+* create a new object from the atoms for which you just measured a property
-ramp_new ramp1, pdbset_1, [ -3, 0, 3]
+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].
-show surface
+* Load the cube file containing the ELF function, e.g. H2O_elf.cube
-set surface_ramp_above_mode
+<gallery perrow=2 widths=250 heights=250>
 = See Also =

← Older revision	Revision as of 14:35, 20 June 2009
(No difference)