How to Use Jmol to Study and Present Molecular Structures, Volume 1Jmol is an interactive viewer for molecular models in the computer. This book aims to be both a tutorial for beginners and a handbook for reference and deepening for more skilled users. It may be of profit for instructors, content authors, students, researchers, and administrators or designers of information portals. The book is organized in sections for a gradual learning curve. It starts with the simplest and most frequent commands and then advances into the occasional, specific and more complex ones. There are sections addressed to those who only need occasional and basic use, another that explains how to take advantage of the command language -split into two levels and further continued on vol. 2- and, finally, a section only needed by those interested on preparing web pages to present models to others. A command index is included, as well as a glossary and a listing of reference addresses in internet, including that of the companion website created for this book. |
Contents
Introduction | 13 |
Obtaining and deploying Jmol | 17 |
Preparation for using Jmol | 19 |
Preparation for using the standalone Jmol application | 20 |
Preparation for using the JmolApplet | 21 |
Obtaining molecular models | 23 |
Models from databases | 24 |
Models from web pages | 25 |
Scripting language Level 2 | 71 |
Loading molecular models ΙΙ | 72 |
Schematic styles ΙΙ | 73 |
Coloring commands ΙΙ | 74 |
Font commands | 78 |
Rendering of multiple bonds | 79 |
Hydrogen bonds and disulphide bonds ΙΙ | 80 |
Orientation of the model | 81 |
Building models | 26 |
Basic operation of the program from the interface | 27 |
Top menu | 28 |
Copying information | 29 |
Mouse and keyboard | 30 |
Advanced options | 31 |
Popup menu | 34 |
Information about the molecule | 35 |
Atom style | 36 |
Schematic renderings for biomolecules | 37 |
Colors | 38 |
Selecting parts of the molecule | 39 |
Hydrogen atoms | 40 |
Measurements | 41 |
Coordinate system and crystallographic information | 42 |
Jmol scripting language | 43 |
Issuing commands | 44 |
Common features for commands and their parameters | 45 |
Scripting language Level 1 | 49 |
Loading scripts | 50 |
Atom size | 51 |
Bond thickness | 52 |
Coloring commands Ι | 54 |
Atom expressions Ι | 55 |
Atom expressions in biomolecules | 57 |
Combining expressions | 62 |
Selecting part of the model | 64 |
Assistance during selection | 66 |
Color of the Jmol panel | 67 |
Bound box | 68 |
Coordinate axes | 69 |
Rotation Ι | 82 |
Translation | 84 |
Size | 85 |
Centering | 87 |
Combined movement | 89 |
Measurements | 92 |
Vibration of the molecule | 95 |
Including Jmol models in a web page Level 1 | 97 |
Jmol initialization | 99 |
Inserting the model | 101 |
buttons links and checkboxes | 102 |
Links | 103 |
Including Jmol models in a web page Level 2 | 105 |
Menus | 106 |
Handling the model based on JavaScript events Ι | 107 |
Including HTML code | 108 |
Coloring the models panel | 109 |
Rectangular panels and panels with relative size | 110 |
Including Jmol models in a web page Level 3 | 113 |
Handling the model based on JavaScript events ΙΙ | 114 |
Saving and restoring model orientations | 115 |
Browser test | 116 |
Including multiple Jmol applets | 117 |
Associating controls with applets | 118 |
Associating commands with applets | 119 |
Integration with CSS cascading style sheets | 120 |
Appendices | 123 |
Glossary | 129 |
| 135 | |
| 137 | |
Common terms and phrases
alpha carbons alpha helix angle angstroms applet applied atom expression axes axis backbone beta strand blue boundBox browser chain chemical element clicking color code Coloring commands coloring scheme controls CSS class currently selected default color defined described disulphide bonds double-click example file formats filename folder font handbook Handling the model hBonds hexadecimal hide Hydrogen bonds identifier Including Jmol models Inserting Java JavaScript Jmol application Jmol panel Jmol scripting language Jmol.js JmolApplet keywords label load located mmcif molecular coordinate file molecular models molecule monitor lines mouse moveTo Note nucleic acids operating system orientation parameters pixels pop-up menu proteins radio buttons RasMol residue ribbons RRGGBB script file script type="text/javascript scripting language secondary structure selected atoms set echo set measure spacefill spheres spin ssBonds standalone program style subsection text displayed translation unit cell unitCell vector vibration volume wireframe zoom zoomTo