Documentation issues - confusing use of "system.file()" within "read.xxx()" function calls

[Barry Grant]

Folks are confused with the use of "system.file()" in the example code from various doc and user guide files (e.g. in the call to "read.dcd()" help etc.).

Note that the use of "system.file()" here is only to find the file path to the example files that ship with the package (and can thus live in different locations on a users machine once the package is installed).

One option is to put these files online and let the read.xxx() functions call them with http. The he downside here is that if a user had no web connection they would get a read error. Either way lets update the doc files to be more clear here.

Specifically mentioned were the user guide on http://thegrantlab.org/bio3d/.

Also the links on this entry (http://bio3d.pbworks.com/w/page/7824481/Tutorials) don't work. CCBP tutorial links broken.