Documents

CueMol2

Tutorial

• CueMol2 GUI tutorial (in Japanese)
  • Translation by Google

Manual

• Documents (translation of Japanese version by Google)

General topics

• Basic of Styles
• Style
• Camera
• How to specify colors (color notations)

Opening/Saving files, etc.

• Open files
• Open scene files
• Open PyMOL session file
• Fetch PDB/density map from servers
• Save files
• Save scene files
• Options for saveing Scene
• Color management (rendering in CMYK mode, etc)

GUI elements

• Main window
  • Tabbed molecular view (MolView)
  • Multiple main window
• Scene panel
  • Renderer group
  • Copy-and-paste of Objects and Renderers
• MolStruct panel
• Selection panel
• Color panel
• Symmetry panel
• Density map panel
• View panel
• Animation panel
• Log display panel
• Sequence display panel

Representations (renderers)

• Common renderer settings
• Renderers for molecules
  • Space-filling representation (cpk renderer)
  • Ball&stick representation (ballstick renderer)
  • Cartoon representation (cartoon renderer)

Molecule modeling

• Merge molecule
• Delete atoms
• Change chain ID
• Change residue number

Tools

• Molecular surface (solvent excluded surface)
  • Creating the molecular surface
  • Display of molecular surface
  • Cross section generation of molecular surface

• Electrostatic potential calculation
  • Installation of APBS and PDB2PQR
  • Electrostatic potential map calculation using APBS

• Molecular superposition
• Automatic extraction of interactions
• Create a new covalent bond
• Protein secondary structure assignment

Rendering to image files

• POV-Ray rendering
  • POV-Ray rendering dialog
  • Rendering of semi-transparent objects
  • About Material
  • Toon rendering
  • Rendering of scenes with a sense of depth using Radiosity method
  • About Lighting and Radiosity method
• Other rendering topics
  • Exporting to PNG images
  • Exporting to POV files (without rendering)
  • Exporting to LuxRender scene files for GI rendering

Scripting interface

• Executing scripts
• Python API
  • High-level API
  • Low-level API

CueMol 1.1

Tutorial

• CueMol1.1 GUI tutorial (in Japanese)
  • Translation by Google
• QScript tutorial (in Japanese)
  • Translation by Excite

Manual

Reference

• Translation by Google