Nenad Ban and the Ribosome

Atomic Models of the 60S and 40S Eukaryotic Ribosomal Subunits in Complex with Initiation Factors 6 and 1 respectively Photograph: Katharina Bohm and Felix Voigts-Hoffmann

From a ribosome and PyMol point of view, Professor Nenad Bans lab page is simply a must read as they summarize a lot of useful information. Continue reading Nenad Ban and the Ribosome

QuteMol tutorial – how to make realistic looking figures in 1 min

Just a short introduction to what could have become the perfect tool for generating high quality realistic renderings of PDB files, QuteMol.

QuteMol is an open source program for high quality molecular visualizations of PDB files only. QuteMol mainly differentiates itself from PyMol by its use of real time ambient occlusion and a incredible intuitive user interface.

As a token of just how easy QuteMol actually is to use, I created the below GIF on my own desktop computer in about 1 min. Continue reading QuteMol tutorial – how to make realistic looking figures in 1 min

PyMol tips: batch mode

I personally think  that the most efficient way to do large amounts of high quality and processor demanding renderings with PyMol is to do it in batch mode.

Continue reading PyMol tips: batch mode

Advanced Pymol Movie

Here I will give a shortish guide to how I made this ribosome movie  with Pymol.

Continue reading Advanced Pymol Movie

segid vs chain ID’s using the ribosome as an example

UPDATE: found this command in pymol

set ignore_case, 0

Which, when set to 0, activates the recognition and differentiation of lowercase and uppercase chain IDs in Pymol thereby circumventing some of the problems working with large molecules in PyMol!

Continue reading segid vs chain ID’s using the ribosome as an example

Update to the “PyMol models and Figures” page!

Did a large update to the “PyMol models and figures” today. I added a lot of different styled figures from my PhD thesis.

My very first PyMol figures

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: Continue reading My very first PyMol figures

A different kind of molecular visualization

My girlfriend drew the below figure in pen by hand, to be used as a cover for a scientific assignment. We then scanned the drawing to as high resolution as our crappy desktop scanner/printer would allow and I processed the drawing using the free raster graphics editor GIMP. Continue reading A different kind of molecular visualization