Users and Contributors guide
Examples
Create a new project
Create a molecule from a sequence
Load a spectrum
Wiki command flowcharts:
Guide for users
The documentation consists of free style text, shown either in the left column in the case of pages with a 2 column layout or in the whole page in a 1 column layout. However, given the complexity of the program, the documentation of analysis has standardised page layouts, command abbreviations and procedures descriptions.
Abbreviations in wiki documentation
Within the text in the left column of a page we use the following abbreviations to indicate menu actions, tabs, command buttons etcetera:
M: Project: New
Enter project name (enter "NapD", click OK)
M: Molecule: Molecules
{Add Sequence}
[Read File] (select NapD.fasta; OK)
[Tidy]
[Add Sequence!]
New Molecule Name (Molecule1; OK)
Mol System code (MS1; OK)
Chain Code (A; OK)
M: Experiment: Open spectra
Navigate to the directory where the data are stored
Select a spectrum
Click [Open spectrum]
For each spectrum: Inspect parameters and click [Commit]
Set the experimental parameters e. g. |Type Synonym| and |Full Type| and end by clicking [Close - All Done] or [Done]
Command flow charts
The command flow charts describe lists of commands or actions in a hierarchical structure and using color schemes:
Window identifiers and menus are colored purple
Tabs are colored green
Input widgets and associated actions are described in red
Some examples is shown in the right column of this page. Since the command flow charts have their own organisation, using the abbreviation structure in the table above is optional.
Guide for contributors
The CCPN team welcomes and encourages any contributions from users to the Analysis documentation on the wiki. Since part of the wiki is intended to become the official release documentation we aim to maintain high quality standards for the documentation. We therefore strongly urge contributors to follow the rules and standards for editing that are listed below. Suggestions and comments are welcome.
Page layout
Alternative 1:
Choose a 2 column layout:
Left column
Extended text and images, free for the editor to choose
Right column
Displays the Command flowchart(s) used to describe a procedure in short, nested in a table
Alternative 2:
Choose a single column layout where the command flowchart(s) is/are placed in the button of the page.
Images
For the sake of speed of the wiki, keep the images of limited file size. In case of screen shots of analysis use jpg format at 85% quality level and resize it to 60% of the original size. For this you can use the linux program mogrify (a convenient command line tool, e.g. : mogrify -resize 60% image.jpg).
Links
For cross referencing, insert wiki links wherever possible to existing wiki pages or external links. In case a page doesn't exist yet, create the new page first, then use the link button to insert that page as a link. Use as much as possible the original page titles for the links, or another clear description of the page it links to.
Command flow charts
Use a hierarchical description of the command flow in indented bulleted lists:
Window identifiers and menus are colored purple
use the exact title as displayed in analysis
Popup windows and tabs are colored green
use the exact title as displayed in analysis
Input widgets and associated actions are described in red
Input widgets are, e.g.:
buttons
pull down lists
text input fields
Associated actions are, e.g.:
select
enter text
double click
confirm
cancel
Use the widget title, the action to perform, and an optional description for entered or selected input values in parenthesis ()
An example is given in the table on the right.
Tips
In order to prevent long loading times, split large topics into several pages with Previous/Next navigation links. This is especially needed in cases where many images are loaded on the page.