In order to use it, you first need to understand a few key concepts:. To be a successful movie director, you also need to know how to “speak the speak”. However, the optional third argument to the load command is the frame index into which the file should be loaded. For example, it is easy to create a movie of a rotating or a rocking molecule. A free cross-platform converter and editor is provides by the ImageMagick suite of programs thanks to J. In this exercise we will generate a molecular morph between two conformations of adenylate kinase. A sequence of structures from a molecular dynamics simulation gives states.
The difference between programs lies in the ease of automation, and the level of control over the creation of image files. We want to animate how this ligand dissociates from the binding pocket while the protein changes conformation to the open state. This is a low-cost movie: An object key frame should automatically be created. For this movie we need two objects:. For example, it is easy to create a movie of a rotating or a rocking molecule.
We will set up our trajectory movie with key frames. You can also press the mclear button on the external GUI window. These image files can then be converted into one movie file. We will learn how to create a simple movie of a small rotating helical peptide. For example, it is easy to create a movie of a rotating or a rocking molecule. The following statements create a sixty frame movie which simply rocks the protein by 10 degrees. Few key words to remember are “states” and “frames”.
Its usage is demonstrated in the following script. The “mdo” command allows you to bind a particular series of PyMOL commands to a frame in tutoriial movie. A free cross-platform converter and editor is provides by the ImageMagick suite of programs thanks to J. You can save the movie using the “mpng” command, or you can save it from the “File” menu.
An object key frame should automatically be created. Each state can be written into an image file, which eventually becomes a movie.
Introduction to Movies with PyMOL
This is more flexible, it allows us to control the mapping per object and do non Tutkrial PDB 1t46 or load it from https: Don’t close PyMOL but continue with the last exercise. Note that 2 seconds correspond to 60 framessince the movie plays with 30 fps frames per second. Jump to frame mdo and mappend: To make thinks little more interesting, we will first custom-build the peptide.
The 1akeA structure has a bound ligand. Hold down the SHIFT key and drag the ligand out of the binding pocket, using the middle mouse button pynol the wheel. Once you have loaded a set of frames into RAM, the frames will remain there until you run the “mclear” command, even if you manipule that model.
A state corresponds to a given three-dimensional tutoria of your system. We tutorrial get a multi-state trajectory-like object. Store another key frame at or near frame 30 by right pymkl on the middle of the movie panel, or type: Somewhat more complex examples can be seen at Cooperativity in Proteins page.
For instance, you can perform a rotation about the axis at each frame of the movie in order to sweep the camera about the object. The “mset” command is used to specify which states get included as frames of a movie. This allows schematic presentation of events like ligand binding or dimer dissociation.
In this exercise we create a movie from a trajectory, which is a multi-state object in PyMOL.
This can be particularly helpful when you’re trying to preserve a movie’s orientation while performing other actions within PyMOL during the same session. State and frame indexes begin with 1, and not 0 as most C and Python programmers would expect. The “util” module includes two python commands for generating mdo commands, “util.
However, the optional third argument to the load command is the frame index into which the file should be loaded. The camera should bounce between ligand view and protein view, and the ligand should appear and disappear.
The following is a Python program with a. Trajectory movie In this exercise we create a movie from a trajectory, which is a multi-state object in PyMOL.
Creating key frames frame: In particular, the mogrify program can annotate a sequence of images, and the convert program will create an MPG movie with the help of the free mpeg2encode program. Some extra trajectory preparation steps will make this look much more pleasant. It will look very jittery.