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, http://www.rcsb.org/pdb/home/home.do). 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 our web pages, presentations, and posters. Please share helpful tips for using Jmol to accomplish this...

Select

Before executing any display commands, you must select what part of the structure 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 #523" ...A is the chain letter).
• select residueNumber-residueNumber - Selects a series of amino acids within a protein
• 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. You can figure out residue numbers by mousing over the backbone region of the amino acid of interest (You'll see something like "[LYS54]:A.CA #523" ...54 is the residue number).
• 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, green, etc. or a 6-digit code for "someColor." See this page for colors and codes: http://jmol.sourceforge.net/jscolors/#JavaScript colors
• 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)

Display

Display: "Cloud" Effects

• isosurface solvent or isosurface molecular - creates a continuous "sheet" over the structure
• color isosurface someColor - Changes the color of the surface. Replace someColor with the name of a color.
• color isosurface translucent - allows you to see through the surface into the molecule. Useful if you still have the backbone displayed, or if ligands are buried inside the structure.
• spacefill someNumber% - Displays all atoms as spheres. Replace someNumber with a value from 1 - 100. Zero erases the space fill.

Display: Only Portions of the Structure

• display #-#:chainLetter - Allows you to display only a sub-section of the structure while hiding the rest of it. Replace the #'s with the range of amino acid residues. Replace chainLetter with the appropriate chain letter (e.g., display 53-95:B)

Display: "Stick" Effects

• wireframe someNumber - Displays all atoms/bonds as sticks. Replace someNumber with a value of at least 50 (50 RasMol units = 0.2 Å).

Frequently Used Command Combinations

String together multiple commands by using a semicolon.

• color_by_chain; 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." I've found that when using the PDB Jmol window, it helps to start the command with color_by_chain

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.