// The purpose of the molecules and descriptions listed here it so links can be
// offered (in the footer of every tutorial page) for further exploration using
// Proteopedia and FirstGlance in Jmol.

// We strongly recommend that you provide below a list of the molecules that appear
// in this tutorial. If you do not want to show such a list, set
// showListOfMolecules to false.

var showListOfMolecules = true;

// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
// PDB Codes or URL's
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 

var moleculeCoordinates = new Array();

// Specify the PDB identification codes, or (if you are using modified or
// unpublished atomic coordinate files) the filenames for the molecules
// that appear in your tutorial, namely the PDB codes or filenames for
// the files in jtat/tutorial_name/js4all/molecules4all.
// There should be one moleculeCoordinates[N] line for each file.

// Do not use index 0. Start with index 1.
// You can remove lines or add more lines, but be sure to keep the indices
// numbered in order, 1-N. To see a completed sample of this file, look in
// jtat/jtatdemo/js4all/molecules.js.

// If the molecule in the tutorial is available from the PDB, please
// simply specify its PDB identification code. Only if it is not available
// from the PDB, then give its filename. Only filenames are permitted here.
// Full URL's (addresses beginning http://) are not permitted.

// Format for a PDB code: "1d66"
// Acceptable formats for a PDB file not available from the PDB:
// "1r3j_opm.pdb" (modified by Orientations of Proteins in Membranes)
// "1s0v_2.mmol" (modified by EBI's Probable Quaternary Structure)
// "1d66_dna_only.pdb" (custom modification)
// If the PDB file is not derived from a published entry at the PDB,
// the first four characters of the filename should NOT be a valid
// PDB code. If they are, that
// PDB code will be used for a link to Proteopedia.

moleculeCoordinates[1] = "1d66";
moleculeCoordinates[2] = "1osl";
moleculeCoordinates[3] = "1l1m";
moleculeCoordinates[4] = "1pyi";
moleculeCoordinates[5] = "2hu4";
moleculeCoordinates[6] = "1s0v_2.mmol";
moleculeCoordinates[7] = "2z8y";
moleculeCoordinates[8] = "1acf";
moleculeCoordinates[9] = "1r3j_opm.pdb";


// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
// DESCRIPTIONS
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 

var moleculeDescription = new Array();

// Please provide a brief description of each molecule, starting with the
// name of the molecule, and including any pertinent details.

// Do not use index 0. Start with index 1.
// You can remove lines or add more lines, but be sure to keep the indices
// numbered in order, 1-N. 
// Do not end descriptions with a period. Appropriate punctuation will be
// automatically added at the end.

moleculeDescription[1] = "Yeast transcription factor Gal4 complexed with DNA (DNA-binding domain only)";
moleculeDescription[2] = "<i>E. coli</i> lac operon repressor bound nonspecifically to DNA";
moleculeDescription[3] = "<i>E. coli</i> lac operon repressor bound specifically to the natural operator O1 DNA";
moleculeDescription[4] = "Yeast transcription factor PPR1 complexed with DNA (DNA-binding domain only";
moleculeDescription[5] = "Bird flu neuraminidase N1 complexed with tamiflu";
moleculeDescription[6] = "Bacteriophage T7 RNA polymerase with RNA template and DNA product";
moleculeDescription[7] = "Carbon monoxide dehydrogenase/Acetyl CoA synthase";
moleculeDescription[8] = "Profilin: an actin-binding protein involved in microfilament dynamics";
moleculeDescription[9] = "Potassium channel, a transmembrane protein, with the membrane boundaries represented by planes of pseudo-atoms";

// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
// CHAPTERS (Optionally, list the numbers of chapters in which the molecules
// are displayed. Important when you have more than a few molecules in one
// tutorial. You can leave these undefined or blank.
// Example: if molecule 2 appears in Chapters 1, 3, and 4:
// moleculeChapters[2] = "1, 3, and 4";
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 

var moleculeChapters = new Array();

moleculeChapters[1] = "1, 4, 5, 6, and 8";
moleculeChapters[2] = "3";
moleculeChapters[3] = "3";
moleculeChapters[4] = "4 and 8";
moleculeChapters[5] = "2";
moleculeChapters[6] = "7";
moleculeChapters[7] = "7";
moleculeChapters[8] = "7";
moleculeChapters[9] = "7";

// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
