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_...
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...
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 ...
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, sc311 and sc11...
If you don’t want your structure looking like clown vomit, enter the following into the command line: isomesh mesh1, 1w5x_2fofc 9) mesh1 -> C -> grays -> gray70 How to di spl ay El ectron Densi ty Server resul ts i n PyMol ...