Fellow PyMol Users
Although I like using PyMol, I would like to submit a gripe about the severe lack of a decent PyMol manual.
A deeper description of the program's features is required if people are seriously going to use PyMol for tricky things beyond simple visualization (simple visualization programs are ten-a-penny and PyMol could be so much more)
Particularly lacking are details of structural editing (mutation, bond rotation, cut-and-paste etc.), interfaces (if any exist) to routines for enegy minimization and a detailed description of the Python command line interface with examples of scripting and how to extend PyMol's capabilities.
By neglecting to adequately document what may be a really useful program, the PyMol user community might fail to attract the kind of user base and support that it deserves and that it needs to ensure its success.
A good, clear and well-thought out manual really helps to make a case for using a particular piece of software (and it might also lower the odds of PyMol having to join the gray legions of commercial "payware").
EMD Lexigen Research Center