PyMOL users who are unable to sponsor the project by purchasing a PyMOL license and maintenance subscription are welcome to use Open?Source versions of PyMOL and any free documentation that can be found on the internet. A tutorial on using PyMOL to generate publication quality figures. Through this tutorial, you will be able to generate the following figures: PyMOL> select active_water, ( (resi 38 and name ND2 and chain A) around 3.5) and (resn HOH) Pymol-!Tutorial!! Go!to!www.rcsb.org.This!is!the!Protein!Data!Bank!(PDB)!=!adatabasefor!protein!structures.!!!!! The!first!thing!we!are!doing!now!is!to!search!for Tutorial on molecular visualisation Version: 26th January 2014 Contents starting the tutorial you need to go the PyMOL menu bar and select Mouse! 2 Button Viewing. 1.3 Structural databases Although it may be easy to build small molecules (see section2), quite often you need to obtain It is compatible with PyMOL version >= 0.99 and it has been tested on both unofficial and official PyMOL builds distributed by Schrodinger. A series of introductory tutorials and in-depth information about all the PyMod 2.0 functionalities can be found in its User's Guide. Pymol-'Tutorial' Zoomed side-by-side comparison between the pymol image and the ray-traced image: note the jagginess of the original image and the smooth appearance of the ray-traced image, with shadows as a bonus. For this part of the tutorial, run PyMol again (or click File->Reinitialize in the external GUI menu), then download and load "1X1R.pdb" View the molecule in sticks representation. PyMol has some useful color commands. First try "Color by chain" which colors each chain in a different color. The purpose of this tutorial was to introduce the computer architecture community to the features and capabilities of two new Python-based frameworks: PyMTL (published in MICRO'14) and Pydgin (published in ISPASS'15). next > < previous View Notes - 1-PyMOL Tutorial from BIO G 101-