Make a movie 3.1 Create individual PDB files from the DCD fileįirst, we split the DCD file into individual PDB files. All input and script files are already contained in each directory. Although the sample does not include water molecules in the system, you can use the same protocol even in the presence of explicit solvent. This is an MD trajectory of a small protein, and the trajectory contains 100 frames.
Let’s download sample PDB and DCD files to be used in this tutorial ( ).
If you don’t want to show a simulation time in the movie, you can skip Step3. Finally, we combine all images using the ffmpeg command to make a move file. In Step3, we write a simulation time in each image using the convert command again through a script. In Step2, we make a png image for each snapshot by executing PyMol through a script. In Step1, DCD file obtained from the MD simulation is split into individual PDB files using the crd_convert tool in GENESIS. Our scheme is composed of four steps, which are outlined in the following figure. The convert command is available in the Imagemagick software package. We use not only GENESIS but also convert and ffmpeg commands.
#Pymol tutorial scripts how to
In this tutorial, we explain how to make a movie file using PyMol, which is one of the popular molecular viewers in the structural biology. In order to play a movie in the presentation, we should create a movie file from MD trajectories, and embed it into the slide. How to make a simulation movie with PyMol?Ĭomputational chemists often show simulation movies in their oral presentation in the meeting, conference, or symposium.
0 kommentar(er)
