Difference between revisions of "Main Page"

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|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
 
|+ style="font-size:210%; font-weight: bold; color:#032d45; 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.
 
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
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| New accounts: email jason (dot) vertrees (@) gmail dot com
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| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
 
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| [http://pymol.org PyMOL v1.8.2 has been released] on April 20, 2016.
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Revision as of 12:08, 15 September 2016

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 v1.8.2 has been released on April 20, 2016.
New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
New Plugin LiSiCA is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
Official Release PyMOL v1.8.0 has been released on Nov 18, 2015.
PyMOL Open-Source Fellowship Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
Official Release PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released on May 4, 2015.
New Plugin PyANM is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
New Plugin Bondpack is a collection of PyMOL plugins for easy visualization of atomic bonds.
New Plugin MOLE 2.0 is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
3D using Geforce PyMOL can now be visualized in 3D using Nvidia GeForce video cards (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.
Older News See Older News.
Did you know...

Color h

= Overview =

This script colors the selection passed in based on the hydrophobicity scale as defined by:

Source: http://us.expasy.org/tools/pscale/Hphob.Eisenberg.html
Amino acid scale: Normalized consensus hydrophobicity scale
Author(s): Eisenberg D., Schwarz E., Komarony M., Wall R.
Reference: J. Mol. Biol. 179:125-142 (1984)

Or check out hydrophobicity coloring, with rTools from Kristian Rother. http://www.rubor.de/pymol_extensions_de.html

The Code

<source lang="python">

  1. color_h
  2. -------
  1. PyMOL command to color protein molecules according to the Eisenberg hydrophobicity scale
  2. Source: http://us.expasy.org/tools/pscale/Hphob.Eisenberg.html
  3. Amino acid scale: Normalized consensus hydrophobicity scale
  4. Author(s): Eisenberg D., Schwarz E., Komarony M., Wall R.
  5. Reference: J. Mol. Biol. 179:125-142 (1984)
  7. Amino acid scale values:
  9. Ala: 0.620
  10. Arg: -2.530
  11. Asn: -0.780
  12. Asp: -0.900
  13. Cys: 0.290
  14. Gln: -0.850
  15. Glu: -0.740
  16. Gly: 0.480
  17. His: -0.400
  18. Ile: 1.380
  19. Leu: 1.060
  20. Lys: -1.500
  21. Met: ..→
A Random PyMOL-generated Cover. See Covers.


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