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.