We distribute a number of extended Bio3D vignettes that provide worked examples of using Bio3D to perform a particular type structural bioinformatics analysis. An updated list of these can be found on-line.
At the time of writing these include:
There is also extensive on-line documentation with worked examples (and their output) for all functions and a package manual (in PDF format) that is a concatenation of each functions documentation (without example output).
Note that for information on Bio3D development status or to report a bug, please refer to: https://bitbucket.org/Grantlab/bio3d