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== PyMol Wiki Home ==
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You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.
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|+ style="font-size:210%; font-weight: bold; color:#000000; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
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| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
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*** [[Windows]]
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*** [[Script Library]]
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! Python 3
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
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! POSF
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| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
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! Tutorial
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! New Plugin
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| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
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|-
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! Selection keywords
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| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
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|-
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! Plugin Update
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| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
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! New Script
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| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
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|-
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! Older News
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| See [[Older_News|Older News]].
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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
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* [[NMR Applicaitons]] (Doug Kojetin)
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|}
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* [[Plugins/Modules]] (Doug Kojetin)
 
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** [[APBS Plugin]]
 
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* [[Plugins]] (Michael George Werner)
 
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** [[List of Plugins]]
 
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** [[Structure Alignment Editor]]
 
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[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
 
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Latest revision as of 03:21, 22 June 2021

hosted by SBGridlogo2.jpg
Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
To request a new account, email SBGrid at: accounts (@) sbgrid dot org
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
Official Release PyMOL v2.5 has been released on May 10, 2021.
Python 3 New Python 3 compatibility guide for scripts and plugins
POSF New PyMOL fellows announced for 2018-2019
Tutorial Plugins Tutorial updated for PyQt5
New Plugin PICv is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
Selection keywords New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll!
Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL
New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
Older News See Older News.
Did you know...

Surface ramp above mode

The surface_ramp_above_mode setting is for coloring molecular surfaces by electrostatic potential, using a color ramp. If on, the surface is colored by the potential on the solvent accessible surface, which is one solvent radius above the surface.

Coloring with surface_solvent=0 and surface_ramp_above_mode=0 is less meaningful, since a solvent or ligand atom never reaches the molecular surface of the protein (only the accessible surface). Furthermore, surface_solvent=1 with surface_ramp_above_mode=1 isn't meaningful either.

Illustration

Surface ramp above mode.jpg

Example

load molecule.pdb
load electrostaticmap.dx

ramp_new espramp, electrostaticmap, [ -3, 0, 3]

show surface

set surface_color, espramp
set surface_ramp_above_mode

See Also
A Random PyMOL-generated Cover. See Covers.


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