my PyMOL examples

Here is the summary page for PyMOL examples I made in the past few years.  I made this summary for me and people to easily find some PyMOL scripts/commands. Hope this summary list helps you 🙂

• Features
  • Grid mode
  • Customize spectrum/gradient colors
  • Morphing movie using RigiMOL/PyMOL
  • compute molecular weight
• DNA
  • display different modes of rings and backbone
    • Examples to display RNA or DNA backbone
    • Draw filled ring, different mode of backbone and ray_trace modes (new post in 2011)
    • Different colors of nucleotide rings in DNA/RNA
    • draw filled ring and ribbon of backbone (2006)
    • examples scripts of transparent surface and backbone (written in Chinese)
• Proteins
  • [PyMOL] molmol-like colored secondary structures
  • Draw Goodsell-like view rendering by GLSL (may require version 1.5 or later)
  • Contact Map view (CMView), a JAVA contact map visualizer running with PyMOL.
  • Manually assign the secondary structural regions (new, 2011)
  • customized length and width (or thickness) of helices and strand
  • examples of some cartoon commands (fancy helices, discrete color, highlight color..)
  • side-chain helper
  • examples of ray_trace
  • gradient background color (only for PyMOL 1.4 or newer)
  • electrostatic surface potential/charges
  • side-by-side comparison of 3 electrostatic surface potentials 
  • make movies (links only)
  • pynmr — an extension of NMR structures
  • make a box for proteins
  • color protein structure based on “B factor”
    • script to add values of B-factor into PDB file
  • old fashion black-white monochrome cartoon view
  • sausage view of protein structures
  • align proteins (command: align)
  • display disulfide bond (out of date, done in 2006)
  • introduction of “sequence mode”
  • define secondary structure by your model (written in Chinese)
  • Split NMR ensemble into multiple states in PyMOL (written in Chinese)
  • example of transparent surface and cartoon of protein (written in Chinese)
  • very simple cartoon view (written in Chinese) (done in 2006)