PYMOL MOVIE TUTORIAL
If you are compressing movies using Adobe Premiere recommended for best quality , you will probably want to convert the files using ImageMagick or a similar package into a format that Premiere is capable of reading such as “. We want to animate how this ligand dissociates from the binding pocket while the protein changes conformation to the open state. You can save movie images to numbered PNG format files with a common prefix. 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. However, the optional third argument to the load command is the frame index into which the file should be loaded. Trajectory movie In this exercise we create a movie from a trajectory, which is a multi-state object in PyMOL. To make thinks little more interesting, we will first custom-build the peptide. PyMOL has the ability to cache a series of images in RAM and to play them back at a much higher rate than they could be rendered originally.
Note that 2 seconds correspond to 60 frames , since the movie plays with 30 fps frames per second. Converting a sequence of images into a movie can be achieved by many different means depending on the operating system and the available software. Go to frame 30, using the movie slider, or by typing: Here a static structure is subject to a gentle rock. Fortunately, there are several excellent tutorials online that demonstrate how to create movies with PyMOL. One for the protein, and one for the ligand. It will look very jittery.
PyMOL has the ability to cache a series of images in RAM and to play them back at a much higher rate than they could be rendered originally. See “help load” or consult the reference section for more information. Once you have loaded a set of frames into RAM, the frames will remain there until you run the “mclear” command, even pyoml you manipule that model.
In this exercise we will do a simple ligand dissociation animation. The camera should ttuorial between ligand view and protein view, and the ligand should appear and disappear.
You get to direct a movie that rotates the peptide!
PyMOL Moviemaking Tutorial
State and frame indexes begin tuttorial 1, and not 0 as most C and Python programmers would expect. Relevant commands for scripting mset and pyoml The 1akeA structure has a bound ligand. Either way, you must provide a prefix which will be used to create numbered PNG files.
The movie panel allows interactive inserting and deleting of frames, as well as moving and copying of key frames. Every state represents a different conformation of the same molecule.
PyMOL Moviemaking Tutorial
In order to use it, you first need to understand a few key concepts:. By default, each new file loaded will be appended onto the object’s states. The “mdo” command allows you to bind a particular series of PyMOL commands to a frame in the movie.
Timeline editing The speed of interpolations depends on the number of frames between two key frames. The following is a Python program with a. In this exercise we create a movie from a trajectory, which is a multi-state object in PyMOL. This exercise is similar to the previous one, but we will add style information with scenes. The following statements create a sixty frame movie which simply rocks the protein by 10 degrees. To change the speed after you have created key frames, you can move key frames or insert additional frames at any given frame.
Fetch PDB 1t46 or load it from https: 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.
Scenes store the camera view, object and atom colors, representations, and which objects are enabled. You can play the movie now.
Few key words to remember are “states” and “frames”. These image files can then be converted into one movie file. Here a static structure is subject to a gentle rock.
A molecule frames “time” on the movie panel ttuorial least two key frames with different camera orientation Open PyMOL and follow these steps: See “help mmatrix” or the reference section for pymkl information. If you load states into an object with a state index of 0, you are indicating that you want the state to be appended after the last existing state in the object. A free cross-platform converter and editor is provides by the ImageMagick suite of programs thanks to J.
One for the protein, and one for the ligand. Since both molecules will be in the same object after loading 1t See “help mdo” or the reference section for more information.
MovieSchool – PyMOLWiki
You can save the movie using the “mpng” command, or you can save it from the “File” menu. Each state can be written into an image file, which eventually becomes a movie.
This gives a global tjtorial In this exercise we will generate a molecular morph between two conformations of adenylate kinase. This allows schematic presentation of events like ligand binding or dimer dissociation.
It will look very jittery.