Haynes:Jmol Guide

The solved 3D structures for thousands of proteins (many of which are used in our work) are available at the Protein Data Bank (PDB). These are useful for investigating protein structure and function, and for discovering/ designing new modular (BioBrick) parts.

Different regions of the protein, its ligands, subunits, and physical properties can be displayed in different colors, renderings, etc. to make informative images for your web pages, presentations, and posters. Please share helpful tips for using Jmol to accomplish this...

Select

Before executing any display commands, you'll want to specify what you want to change.

Select: Proteins & Ligands

• select protein or select amino - Selects all proteins in the structure
• select :chainLetter - Selects a single contiguous peptide in multi-part protein complexes. Substitute a letter (a, b, c, etc.) for "chainLetter". You can figure out chain letters by mousing over the chain of interest (You'll see something like "[LYS54]:A.CA #543" ...A is the chain letter).
• select residueNumber:chainLetter - Selects an amino acid residue within a chain. Substitute "residueNumber" with the number of the amino acid in the protein chain, and "chainLetter" with a, b, c, etc.
• select helix - Selects all alpha helices
• select sheet - selects all beta sheets
• select hetero - Selects water, ions, and ligands (heterogenous atoms)
• select ligand - Selects all ligands

Select: Nucleic Acids (DNA/ RNA)

• select dna - Selects all DNA
• select rna - Selects all RNA
• select nucleic - Selects all nucleic acids

Select: General Features

• select: all - Selects the entire structure.

Color

Commands for changing the color of the selected regions.

• color someColor - Substitute red, blue, yellow, orange, etc. for "someColor."
• color CPK - Sets the color of the selected region to follow the CPK convention. Hydrogen = white, Carbon = black, Nitrogen = blue, Oxygen = red, etc. (See http://en.wikipedia.org/wiki/CPK_coloring)

Frequently Used Command Combinations

String together multiple commands by using a semicolon.

• select :chainLetter; color someColor - Change the color of a subunit/ chain. Substitute A, B, C, etc. for "chainLetter". This selects a single contiguous peptide in multi-part protein complexes. Substitute red, blue, yellow, orange, etc. for "someColor."

Resources

• An Introduction to Jmol Scripting - Very helpful interactive tutorial that lets you click buttons to see how different command lines change the appearance of a 3D structure. By Nathan Silva and David Marcey.