// =========================================================================== // This file, chapter.js, must be provided for each chapter.htm. // Each chapter.js file contains the settings and content for one chapter. // Each chapter should be in a separate directory (folder). // Each chapter directory should contain one and only one chapter.htm file. // // Lines beginning "//" are comments for authors. They are ignored by JTAT. // =========================================================================== // ========== SECTION I: PROVIDE SLIDERS? ============ // These control whether this Chapter has a Slab ("Cut") // slider, in addition to a Zoom slider, or neither. // You cannot have a Slab slider without also having the Zoom slider. // The label on the slab slider (typically "Cut" or "Slab") // is defined in _jsutil/config2.js showZoomSlider = true; showSlabSlider = false; // ========== SECTION II: CHAPTER TITLE, INTRODUCTION ============ // CHAPTER TITLE IS REQUIRED chapterTitle = 'Color Schemes: DRuMS'; // CHAPTER SUBTITLE IS OPTIONAL chapterSubtitle = ''; // OPTIONAL INTRODUCTION FOR THIS CHAPTER // Be sure to include paragraphs within

tags. This gives them margins. chapterIntro = '

\n\ \n\ Careful selection of colors can help your structural views communicate \n\ effectively, and enhance their attractiveness. Except when there are \n\ compelling reasons to do otherwise, we recommend that you use the standard \n\ color schemes built into JTAT, which are based upon a standard named \n\ DRuMS. \n\ Below are examples illustrating these color schemes. \n\ \n\

\n\ \n\ JTAT makes it easy to use these color schemes by providing scripts to \n\ color your molecules, ready-made color keys to explain your molecular \n\ views, and style sheets so you can apply the standard colors to text by \n\ naming them. For details on how to use these, please see the \n\ Instructions for Authors. \n\ \n\ <\/p> \n\ '; // ========== SECTION III: NAVIGATION (NEXT, PREVIOUS, CONTENTS, RESET) ============ // The 3 URL's below must be relative to the current chapter. // The position and style of the navigation bar are set in config.js // Leave blank if there is only one chapter, and no contents page. contentsButtonGoesTo = "../contents/contents.htm"; // If the View buttons define the orientation/zoom, // no Reset button is needed, so provideResetButton should be false. // In contrast, some chapters are designed to maintain the orientation and // zoom set previously by the user when a new view is displayed. // These need a Reset button, so provideResetButton should be true. // When provided, a Reset button runs reset.spt in the chapter's directory. // It allows Reset to do something different than the "View 1" button does. provideResetButton = false; // ignored when isContents. // Leave blank if this is the first chapter. previousChapterButtonGoesTo = "../ch_spin/chapter.htm"; // Leave blank if this is the last chapter. nextChapterButtonGoesTo = "../ch_bkg/contents.htm"; // ========== SECTION IV: MOLECULAR VIEW BUTTONS ============ // Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== ===== setupButton(1, // NUMBER OF MOLECULES "../molecules4all/1s0v_2.mmol", // ATOMIC COORDINATE FILE "script view01.spt;", // VIEW SCRIPT blackBackground, // BACKGROUND (blackBackground or whiteBackground) spinningOff); // SPINNING (spinningStart/On/Same/Off) // @@ spinningStart above! //+ composition_key(".") + // MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iButtonText] = 'Composition: \n\

\n\

\n\ '; // MOLECULAR VIEW DETAILS buttons[buttonNumber][iDetailsTitle] = 'What Is This Molecule? Checkboxes.'; buttons[buttonNumber][iDetailsText] = 'Not very many molecules in the \n\ Protein Data Bank \n\ have all five of protein, DNA, RNA, ligand, and solvent. This one \n\ is bacteriophage \n\ T7 DNA-dependent RNA polymerase (1s0v). \n\ In this crystal structure, the \n\ asymmetric unit \n\ contained four copies. Shown here is \n\ copy 2, \n\ separated by \n\ EBI\'s Probable Quaternary Structure Server. \n\

\n\ \n\ Checkboxes to modify a view are an advanced option of JTAT. \n\ See \n\ Jmol Controls. \n\ Because the checkbox labels serve as a color key, the javascript \n\ function composition_key() was not used here. \n\ \n\ '; // TEXT AFTER MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iPostButtonText] = '

\n\ Script: script ../../_drums/composition.spt \n\
\n\ Color Key: composition_key(".") \n\

\n\ '; // Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== ===== setupButton(1, // NUMBER OF MOLECULES "../molecules4all/2z8y_elements.pdb", // ATOMIC COORDINATE FILE "script view01a.spt;", // VIEW SCRIPT blackBackground, // BACKGROUND (blackBackground or whiteBackground) spinningStart); // SPINNING (spinningStart/On/Same/Off) // MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iButtonText] = 'Chemical Element: ' + element_key("c,alphac,n,o,s,fe,cu,ni,xe", "", "."); // MOLECULAR VIEW DETAILS buttons[buttonNumber][iDetailsTitle] = 'What Is This Molecule?'; buttons[buttonNumber][iDetailsText] = 'This amazing cluster occurs in carbon monoxide \n\ dehydrogenase/acetyl-CoA synthase(CODH/ACS, \n\ PDB code 2z8y) \n\ from Moorella thermoacetica. It contains two active sites \n\ connected by a one of the longest known intramolecular channels \n\ (138 Å). The first site produces CO from carbon dioxide. \n\ The CO is used at the second site in the synthesis of acetyl-CoA. Xenon was used to \n\ confirm the location of this channel. To see the channel, view \n\ 2z8y in Proteopedia, and click on Xe under Ligands. \n\ '; // TEXT AFTER MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iPostButtonText] = '

\n\ Script: color cpk \n\
\n\ Color Key: element_key("c,alphac,n,o,s,fe,cu,ni,xe", "", "."); \n\

\n\ '; //Color Key: element_key("c,o,n,s,fe,ni,cu,xe", ".") \n\ // Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== ===== setupButton(1, // NUMBER OF MOLECULES "../molecules4all/1acf.pdb.gz", // ATOMIC COORDINATE FILE "script view02.spt;", // VIEW SCRIPT blackBackground, // BACKGROUND (blackBackground or whiteBackground) spinningSame); // SPINNING (spinningStart/On/Same/Off) // MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iButtonText] = 'Secondary Structure: ' + sst_key("."); // MOLECULAR VIEW DETAILS buttons[buttonNumber][iDetailsTitle] = 'Profilin; Turns?'; buttons[buttonNumber][iDetailsText] = 'The molecule shown here is profilin \n\ (1acf), \n\ an actin-binding protein involved in microfilament dyanamics. \n\ It is unusual that the authors of this model designated the \n\ turns. While it is routine for authors \n\ of protein models to designate alpha helices\n\ and beta strands, turns \n\ are specified in only about 4% of models in the PDB. Jmol shows \n\ secondary structure according to the HELIX, SHEET, and TURN records \n\ placed in the PDB file header by its authors. As of summer, 2008, \n\ Jmol\'s internal calculation of secondary structure is flawed. The best \n\ way to color turns in models lacking TURN records is to add such records. \n\ '; // TEXT AFTER MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iPostButtonText] = '

\n\ Script: color structure \n\
\n\ Color Key (with Turn): sst_key(".") \n\
\n\ Color Key (without Turn): ss_key(".") \n\

\n\ Script: script ../../_drums/polarity2.spt \n\
\n\ Color Key: polarity2_key(".") \n\

\n\ '; // Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== ===== setupButton(1, // NUMBER OF MOLECULES "../molecules4all/1r3j_opm.pdb", // ATOMIC COORDINATE FILE "script view04.spt;", // VIEW SCRIPT blackBackground, // BACKGROUND (blackBackground or whiteBackground) spinningSame); // SPINNING (spinningStart/On/Same/Off) // MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iButtonText] = 'Potassium channel (1r3j) showing how the extensive hydrophobic \n\ region encircling the molecule fits between the predicted \n\ extracellular and \n\ intracellular lipid membrane/water boundaries. \n\ '; // MOLECULAR VIEW DETAILS buttons[buttonNumber][iDetailsTitle] = 'Membrane Planes'; buttons[buttonNumber][iDetailsText] = 'Prediction of the membrane planes was done by the Orientations \n\ of Proteins in Membranes (OPM) Server, courtesy of the University \n\ of Michigan. This model, containing pseudo-atoms representing the \n\ predicted membrane planes, was downloaded from \n\ OPM\'s page on the potassium channel. \n\ '; // TEXT AFTER MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iPostButtonText] = '
\n\ \n\ For instructions on how to apply \n\ arbitrary \n\ colors \n\ to text, please see the \n\ Instructions for Authors. \n\ \n\ '; // Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== ===== setupButton(1, // NUMBER OF MOLECULES "../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE "script view05.spt;", // VIEW SCRIPT blackBackground, // BACKGROUND (blackBackground or whiteBackground) spinningSame); // SPINNING (spinningStart/On/Same/Off) // MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iButtonText] = 'Protein charge: \n\
\n\ ' + aacharge_key(", ") + dna_key(".") + ' \n\

\n\ Script: script ../../_drums/aacharge.spt \n\
\n\ Color Keys: aacharge_key(", ") + dna_key(".") \n\

\n\ Please notice that the protein surface contacting the \n\ DNA has only \n\ positive charges, complementing \n\ the negatively charged phosphate backbone of the \n\ DNA. \n\

\n\ '; // MOLECULAR VIEW DETAILS buttons[buttonNumber][iDetailsTitle] = 'Entire sidechains'; buttons[buttonNumber][iDetailsText] = ' \n\ Entire sidechains are colored because quite often, the charged \n\ atoms at the ends of sidechains are missing due to disorder in the protein crysal. \n\

\n\ Note that this script colors \n\ His \n\ in addition to \n\ Lys, \n\ Arg, \n\ Asp, \n\ and \n\ Glu \n\ even though \n\ His \n\ has only a partial positive charge at neutral pH. \n\ \n\ '; // TEXT AFTER MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iPostButtonText] = ''; // Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== ===== setupButton(1, // NUMBER OF MOLECULES "../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE "script view06.spt;", // VIEW SCRIPT blackBackground, // BACKGROUND (blackBackground or whiteBackground) spinningSame); // SPINNING (spinningStart/On/Same/Off) // MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iButtonText] = 'Protein charge and polarity in 4 colors: \n\

\n\ ' + polarity4_key(", ") + dna_key(".") + '

\n\

\n\ Script: script ../../_drums/polarity4.spt \n\
\n\ Color Keys: polarity4_key(", ") + dna_key(".") \n\

\n\ '; // MOLECULAR VIEW DETAILS buttons[buttonNumber][iDetailsTitle] = 'Entire residues are colored.'; buttons[buttonNumber][iDetailsText] = ' \n\ In this Polarity4 color scheme, entire amino acids are colored according to the \n\ charges of their sidechains, in order to avoid needing a fifth color \n\ for backbone (see Polarity5, next). \n\ \n\ '; // TEXT AFTER MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iPostButtonText] = ''; // Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== ===== setupButton(1, // NUMBER OF MOLECULES "../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE "script view07.spt;", // VIEW SCRIPT blackBackground, // BACKGROUND (blackBackground or whiteBackground) spinningSame); // SPINNING (spinningStart/On/Same/Off) // MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iButtonText] = 'Protein charge and polarity in 5 colors: \n\

\n\ ' + polarity5_key(", ") + dna_key(".") + '

\n\

\n\ Script: script ../../_drums/polarity5.spt \n\
\n\ Color Keys: polarity5_key(", ") + dna_key(".") \n\

\n\ '; // MOLECULAR VIEW DETAILS buttons[buttonNumber][iDetailsTitle] = 'Sidechains are colored.'; buttons[buttonNumber][iDetailsText] = ' \n\ In this Polarity5 color scheme, amino acid sidechains are colored. \n\ Backbone, while it is polar, uncharged, is given a distinct color \n\ because most of its hydrogen bonding needs are met internally by \n\ secondary structure interactions. Therefore, on average, it is less available \n\ for hydrogen bonding with non-backbone atoms than are polar sidechain atoms. \n\ \n\ '; // TEXT AFTER MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iPostButtonText] = ''; // Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== ===== setupButton(1, // NUMBER OF MOLECULES "../molecules4all/1s0v_2.mmol", // ATOMIC COORDINATE FILE "script view08.spt;", // VIEW SCRIPT blackBackground, // BACKGROUND (blackBackground or whiteBackground) spinningSame); // SPINNING (spinningStart/On/Same/Off) // MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iButtonText] = 'Nucleic acid sequence: \n\

\n\ ' + nucbases_key(".") + '

\n\

\n\ Script: script ../../_drums/nucbases.spt \n\
\n\ Color Key: nucbases_key(".") \n\

\n\ This view shows only the DNA and RNA from the T7 polymerase shown \n\ in View 1 (1s0v). Can you tell which chain is RNA? (Look for the \n\ single Uracil.) \n\

\n\ '; // Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== ===== setupButton(1, // NUMBER OF MOLECULES "../molecules4all/1s0v_2.mmol", // ATOMIC COORDINATE FILE "script view09.spt;", // VIEW SCRIPT blackBackground, // BACKGROUND (blackBackground or whiteBackground) spinningSame); // SPINNING (spinningStart/On/Same/Off) // MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iButtonText] = 'Nucleic acid base sequence vs. backbone: \n\

\n\ ' + nucbasesbb_key(".") + '

\n\

\n\ Script: script ../../_drums/nucbasesbb.spt \n\
\n\ Color Key: nucbasesbb_key(".") \n\

\n\ '; // Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== ===== setupButton(1, // NUMBER OF MOLECULES "../molecules4all/1s0v_2.mmol", // ATOMIC COORDINATE FILE "script view10.spt;", // VIEW SCRIPT blackBackground, // BACKGROUND (blackBackground or whiteBackground) spinningSame); // SPINNING (spinningStart/On/Same/Off) // MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iButtonText] = 'Purines vs. pyrimidines: \n\

\n\ ' + purpyr_key(".") + '

\n\

\n\ Script: script ../../_drums/purpyr.spt \n\
\n\ Color Key: purpyr_key(".") \n\

\n\ '; // Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== ===== setupButton(1, // NUMBER OF MOLECULES "../molecules4all/1s0v_2.mmol", // ATOMIC COORDINATE FILE "script view11.spt;", // VIEW SCRIPT blackBackground, // BACKGROUND (blackBackground or whiteBackground) spinningSame); // SPINNING (spinningStart/On/Same/Off) // MOLECULAR VIEW DESCRIPTION buttons[buttonNumber][iButtonText] = 'Nucleic acid base sequence vs. backbone: \n\

\n\ ' + purpyrbb_key(".") + '

\n\

\n\ Script: script ../../_drums/purpyrbb.spt \n\
\n\ Color Key: purpyrbb_key(".") \n\

\n\ '; // End of View Buttons ===== ===== ===== ===== ===== ===== ===== ===== ===== // CHAPTER CONCLUSION chapterConclusion = ''; // ========== END OF chapter.js ============