or user (power < 0) - sets color to background contrast (black or white) when normalz. for "someColor." I've found that when using the PDB Jmol window, it helps to start the command with color_by_chain returns JSON code for property - allows JavaScript: x Jmol.
Substitute red, blue, yellow, orange, etc. This selects a single contiguous peptide in multi-part protein complexes.
#Color code jmol helix seet software#
Useful if you still have the backbone displayed, or if ligands are buried inside the structure. View molecules with the help of molecular visualization software (Jmol). color isosurface translucent - allows you to see through the surface into the molecule.Replace someColor with the name of a color. color isosurface someColor - Changes the color of the surface.isosurface solvent or isosurface molecular - creates a continuous "sheet" over the structure.Hydrogen = white, Carbon = black, Nitrogen = blue, Oxygen = red, etc. color CPK - Sets the color of the selected region to follow the CPK convention.or a 6-digit code for "someColor." See this page for colors and codes: colors color someColor - Substitute red, blue, yellow, orange, green, etc.select: all - Selects the entire structure.Ĭommands for changing the color of the selected regions.select nucleic - Selects all nucleic acids.select hetero - Selects water, ions, and ligands (heterogenous atoms).select helix - Selects all alpha helices.You can figure out residue numbers by mousing over the backbone region of the amino acid of interest (You'll see something like ":A.CA #523". Substitute "residueNumber" with the number of the amino acid in the protein chain, and "chainLetter" with a, b, c, etc. select residueNumber:chainLetter - Selects an amino acid residue within a chain.
#Color code jmol helix seet series#
select residueNumber-residueNumber - Selects a series of amino acids within a protein.You can figure out chain letters by mousing over the chain of interest (You'll see something like ": A.CA #523". Substitute a letter (a, b, c, etc.) for "chainLetter". select :chainLetter - Selects a single contiguous peptide in multi-part protein complexes.select protein or select amino - Selects all proteins in the structure.The secondary structure is either read from the PDB file (HELIX and SHEET.