How to Use Jmol to Study and Present Molecular Structures, Volume 1

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Lulu.com, 2008 - Computers - 144 pages
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Jmol 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.
 

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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
Reference web addresses
135
Index of commands and keywords
137
Copyright

Common terms and phrases

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