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Tool: Help Viewer (ChimeraX Browser)

The Help Viewer is a built-in HTML browser. ChimeraX help pages are written in HTML and can be shown in this built-in browser using the Help menu, the help command, context menus, and by clicking links from previous commands echoed to the Log. The Help Viewer starts up as a separate window, but can be managed like other ChimeraX panels. It includes a search field and icon buttons for navigation (back, forward, reload), opening a new tab, and adjusting the font size.

An important advantage of the built-in browser is that it provides a simple mechanism to execute ChimeraX commands by clicking special links, for example:

open 1gcn
– encoded as –
<a href="cxcmd:open 1gcn">open 1gcn</a>

** The execution links will only work when the HTML page is shown in the ChimeraX browser, not other web browsers.**

With this mechanism, it is easy to create web pages that use ChimeraX for structure display and other features, as in a scientific presentation or tutorial. Many more command-execution examples can be found in the Quick Start Guide and some of the other ChimeraX tutorials. The javascript in cxlinks.js can be copied and included in the page source to display a brief explanation if such a link is clicked when the page is shown in some other browser.

Web content and HTML files in general (with or without the special command-execution links) can be shown in the ChimeraX browser with commands:

open  URL
– or –
open  local-file.html

Local files can also be opened with File... Open in the menu.

Help Viewer keyboard shortcuts (on Mac, replaces Ctrl):

keyboard shortcutaction
Ctrl-+, Ctrl-=enlarge
Ctrl-0baseline size
Ctrl-topen new tab
Ctrl-wclose current tab
Ctrl-tabnext tab
Ctrl-Shift-tabprevious tab
Ctrl-N (N = 1–8)Nth tab
Ctrl-9last (rightmost) tab

UCSF Resource for Biocomputing, Visualization, and Informatics / August 2019