The animation below demonstrates the photorealistic effect from the ambient occlusion shortcut applied to a protein by entering two letters,AO. This shortcut executes 16 lines of code with the entry of two letters! The animation below demonstrates the submission of two shortcuts,sc311andsc113, se...
EXAMPLE 1: Show hydrogen bonds between protein and docked ligandsEXAMPLE 2: Show hydrogen bonds between two proteinsThere is also a script drawing nice hydrogen bonds from Gareth StockwellWarren DeLanoProtonating ligandsIf your ligands come in with valid valencies and formal charges, PyMOL’s h_...
1、Display a MTZ file in PyMOLApr 26, 2010The following will allow you to create a 2Fo-Fc map using CCP4 from a mtz file to be displayed in PyMOL.1) Start CCP4i, select FFT from the program list or Run FFT Create Map under the Map & Mask Utilities2) This map will cover all ...
in the correct location as described on the download page) the next step is to start up PyMOL.If installed correctly you should see an additional GUI (at right) as shown below:My goal here is to give a basic introduction that will yield a movie that rotates a protein in a full circle...
File -> Open -> 1w5x.ccp4 You will still NOT see electron density, you need to use the mesh command next (see image below). 7) Mesh Displayed: If you don’t want your structure looking like clown vomit, enter the following into the command line: isomesh mesh1, 1w5x_2fofc 9) mes...