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.
Open the VMD and load the coordinate file.
Open Graphice-colors, change the background to white
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 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.
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
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.
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.
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.