Animation of Trajectory with PyMOL and VMD

Introductions of PyMOL

PyMOL is suitable for creating high-quality 3D structural images of small molecules or biological macromolecules (especially proteins). PyMOL is one of the few open source visualization tools available in the field of structural biology.

VMD Tutorial

Open the VMD and load the coordinate file.

Animation of Trajectory with PyMOL and VMD

Open Graphice-colors, change the background to white

Animation of Trajectory with PyMOL and VMD

Display-Axies is set off to turn off the coordinate display.

Open Graphice ---Representions

By Create Rep, you can set different display methods for proteins and ligands separately, where entering Protein in Selected Atoms can display only receptor proteins.

Protein is displayed in two ways:

  • The first one is to set the Coloring Method to Secondary Structure and the Drawing Method to NewCartoon.
  • The second setting of Coloring Method is ColorID solid color display, color can be set to gray according to personal preference, Material set Transparent transparent, Drawing Method is Surf.

The display of ligands is also set by Selected Atoms, which can be set to a particular amino acid with the command resname XXX. XXX is the name of the amino acid in your coordinate file.

Import Trajectory, check the complex and then File>Load Date into Molecule.

Set Renderer to Snapshot, Movie Settings to Trajectory, Format to MPEG-1. Then click Make Movie to start making. The principle is to take a continuous screenshot and then use VideoMach to connect it to video (if your computer does not have VideoMach installed, you need to install it and indicate the path of videomach.exe to VMD).

The animation is finished.

Pymol Tutorials

Open the CMD and cd to the Scripts folder

C:\ProgramData\Anaconda3\Scripts> pip install numpy-1.18.3+mkl-cp38-cp38-win_amd64.whl

ERROR: numpy-1.18.3+mkl-cp38-cp38-win_amd64.whl is not a supported wheel on this platform.

Open pymol's interface

Animation of Trajectory with PyMOL and VMD

The way Pymol displays receptor proteins and ligands is complicated. It does not matter if it is displayed in other ways, but Surface display requires importing two coordinate files with different file names and importing the tracks separately.

>load_traj xxx.xtc,start=1,stop=10000000,interval=20

The receptor protein and ligand are then deleted from the sequence in both coordinates, so that the protein and ligand can be displayed in different modes by showing both coordinates simultaneously.

VideoMach is required for VMD animation, and FFmpeg support is required for Pymol animation. You can install it via pip or conda, or put

ffmpeg.exe, ffplay.exe ,ffprobe.exe

these three executable files can be placed in the environment variable, or in the Scripts folder where Anaconda is located, which itself is in the environment variable.After that, you can create the animation directly.

Animation of Trajectory with PyMOL and VMD

The biggest advantage of Pymol for animation is that it can be displayed with Surface, and in most cases it is more intuitive to display active pockets with Surface.

* For Research Use Only.