Introduction to Felix

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Introduction to Felix 2000

Unix environment

Make sure that your environment is appropriately set up. Either have a statement like
source /usr/msi/cshrc
somewhere in your .cshrc (this will slow down all of your shells, hence not recommended) or alias the insightII, felixX and other MSI programs like this:
alias felix 'source /usr/msi/cshrc; felixX'

Documentation

All Felix documentation is online. We've made these docs searchable and have included search fields in most top level pages. Each section has a very good index which can be accessed from the menu bar across the top of the page. To find info within the somewhat lengthy sections, use the Find feature of your browser.

New to Felix?

If you've never used Felix, you should do some reading: Start with the User Guide and specifically with the Tasks section. Here are a few Tasks subsections that are particularly useful:

The menu interface is exhaustively documented and so is the Felix Command Language Reference
Use the latter when you get stuck with macro programming.

Tutorials

There are a bunch of tutorials although not many of us have ever used them with the exception of the Using Assign tutorial. The latter is essential to understand and use Assign. The tutorials are also available in pdf format.

Assign

The Assign module has a relatively steep learning curve because the philosophy and science behind it are not obvious to most (biomolecular) NMR spectroscopists. The Assign User Interface is well documented. For a quick tour of Assign you will really want to read some of the tasks sections, such as Working with assignment databases, Using connected frames to navigate in multiple spectra within Assign, Spin systems and the sections immediately following the last one.

It is essential that you work through at least part of the Using Assign tutorial. Especially Heteronuclear triple resonance 3D assignment strategy has useful guidance on how to use the more advanced tools in Assign. If you're adventurous or somewhat experienced you might want to go through the tutorials with your own data instead of the supplied stuff.
In any case, only after some getting some background should you attempt to use Assign for real.

In practice we find Assign's project very useful for navigation, even if you don't use any of the assignment tools themselves. Being able to navigate through multiple spectra with ease is well worth setting up a project.

Customization

You can change many aspects of how Felix acts and appears through startup files: Entries in your .Xdefaults file control colors, fonts, default window geometry (size), virtual drawing canvas size and similar things. My favorite settings are:

felix*fontList:                  -adobe-helvetica-bold-r-normal--14-*
#felix*fontList:                 -*-new century schoolbook-*-*-*-*-*-*-*-*-*-*-14-*
felix*background:                LightSeaGreen
felix*foreground:                black
felix*focusoutbackground:        white
felix*focusinbackground:         yellow
felix*highlightcolor:            green
felix*numGDialogs:               1
felix*baloonbackground           blue
felix*baloonforeground          white
felix*RTPDrawingAreaW:           40
felix*RTPDrawingAreaH:           5
felix*RTPScrollbarWidth:         30
felix*RTPDrawingAreaX:           249
felix*RTPDrawingAreaY:           865

felix*zerobuttonforegroundcolor: red
felix.geometry:                  1000x800+60+30
FelixDataBaseViewer*background:  LightSeaGreen
FelixDataBaseViewer*foreground:  black
FelixDataBaseViewer.geometry:    600x400-1-0
RealTimePhase*background:        LightSeaGreen
RealTimePhase*foreground:        black
RealTimePhase.geometry:          -8-8

felix*activeColor:              violetred
felix*normalColor:              DarkSeaGreen4
felix*backgroundColor:  grey65
felix*maxcanvasWidth:   4096
felix*maxcanvasHeight:  4096
felix.RTPgeometry               40x5-2-2

The init.mac file sets Felix internal symbols that let you control cursor color, white-on-black or black-on-white display, pen thickness and slant, and similar parameters. Then it sets the startup process in motion. The .felixrc99 file determines where Felix expects to read and write files. These settings act much like Unix paths.

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links updated March 18, 2002 by Kevin Weiss