This was remedied by adding two other software in the course, one for the “publication quality renderings” ( VMD) and the other for the modeling abilities of side-chain mutations and automated 3D superimposition of structures (Swiss PDB viewer later called DeepView.) Rasmol included a sophisticated line command language but lacked the beautiful “photorealistic” renderings of the workstations. For teaching molecular graphics on the Desktop, I first used Rasmol (see tutorial link below,) which was an amazing software fitting in about half of a 3.5” floppy disk or about 500 kilobytes. I personally used what was called “Unix Workstations” ( Silicon Graphics, sgi) which had powerful graphics and rather beautiful “ photorealistic” renderings.
This class was a useful complement to the main topic of S equence Analysis and (molecular) Evolution also using computers. Ann Palmenberg classes, in particular teaching about molecular graphics on the Desktop at a time when computer use in the classroom was not yet preeminent. Book 4: PyMOL part 3 (Electron Density Maps)įor many years I participated in the teaching of Prof.Book 3: PyMOL part 2 (scripts, animations and movies, multimeric structures, morphing).Book 2: PyMOL part 1 (Graphical representations and atom selection, electrostatic potentials, side-chain mutations, 3D overlays, …).Book 1: Molecular Graphics Essentials (Summary of methods to obtain 3D data file formats).The Biochem 660 PyMOL tutorial book has been split in 4 PDFs for easier read and download:
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