Pymol tutorial how to show ligand interactions

Pymol tutorial how to show ligand interactions how to#

First, you need to ensure the frames are ray traced: Once this has been loaded in, you should smooth over several frames to make the image smooth and less jittery: You shouldnвЂ™t need more than 200 frames, anything larger will start to cause problems for your workstation: Once you have set everything up, it is time to load the trajectory. pml script to ensure I have the same colouring and viewing parameters set for each movie. Now is the time to customise your PyMOL session. Next up, you need to add the co-ordinate. An annoying feature that you often forget until half way through. The easiest way to ensure this happens is to use the trjconv command in GROMACS to produce a. That is to say, all the protein, solvent and ions named in all three. xtc files all need to have the same atoms. Most of the commands you will encounter while making a static structure movie, so should not be too alien.ДЇirstly, you need to load in your structure.

Pymol tutorial how to show ligand interactions how to#

The following tutorial shows you how to turn a static PDB structure into a dynamic one, by adding a GROMACS trajectory. For example: understanding binding events, PPIs over time or even loop motion. This allows your audience to visualise how your protein dynamics evolve over time and a much easier way to explain your results (because, who likes 10,000 graphs in a presentation!? Even if your R plots look super swish.). If you want to take your PyMOL movie making skills to the next level, you should start adding some dynamics data.

But there ends the scope for your static structures. PyMOL plugins, such as emovie.py, help you move beyond the вЂrockвЂ™ and вЂrollвЂ™ scenes in PyMOLвЂ™s movie tab. Static protein movies can enhance an introduction or help users understand important interactions between proteins and ligands. Putting movies into your presentations is the perfect way to cover up a terrible underlying presentation help the audience visualise the systems you are discussing.