Back in 2007 when I was writing my bachelor thesis in macromolecular crystallography I made my very first PyMol rendering. It was off a crystal structure I had solved during my project of elongation factor 2 from yeast. I knew that EF2 contained six domains, so I wanted to visualize the domains boundaries for the readers of the thesis (all two of them). To do this I decided to use PyMol and this was the result:
Not bad for a first time user, however I knew nothing about selection algorithms or res,- seg- or chain-id’s in PyMol, so I manually selected (as in using the mouse only) all the residues belonging to a specific domain one by one, before assigning the selection a specific color and moving on to the next domain. Once I started selecting the residues for the next domain, there was not going back on the colors, as I believed I had to manually re-select all the residues again to change it.
However it got much worse, because I got the idea that I wanted to visualize EF2’s binding to the 70S ribosome relative to the ribosomal subunits. So I did the whole manual selection thing again using the mouse on the two ribosomal subunits and on EF2. It took for ever, but I eventually got this
Again not bad for a first (or rather second) time user. However all my hard work was briefly discarded by my supervisor. He said I should just use a figure from another paper.