In this exercise we will generate a molecular morph between two conformations of adenylate kinase. If you want each frame to be ray-traced, you should turn on raytracing of frames, turn off caching, and clear the cache see the Movie Menu or use the following commands. Hold down the SHIFT key and drag the ligand out of the binding pocket, using the middle mouse button usually the wheel. Imagine a complex movie for a moment, a movie that has camera motions, objects moving independently or in concert with other objects, changing colors and representations. 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. You can save the movie using the “mpng” command, or you can save it from the “File” menu. This tutorial assumes you have some basic knowledge about how to use PyMOL eg. We can do a couple things now, let’s try counting the number of states and frames PyMOL now knows about:.
You can save the movie using the “mpng” command, or you can save it from the “File” menu. 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 “. Jump to frame mdo and mappend: PyMOl supports to patterns for stateSpec. An extra M button should appear for every object in the object menu panel. Trajectory movie In this exercise we create a movie from a trajectory, which is a multi-state object in PyMOL.
PyMOl supports to patterns for stateSpec. Scene based Movie This exercise is similar to the previous one, but we will add style information with scenes. See “help mdo” or the reference section for more information. Go to frame 30, using the movie slider, or by typing: Its usage is demonstrated in the following script.
A molecule frames “time” on the movie panel at least two key frames with different camera orientation Open PyMOL and follow these steps: So, now you see why it’s necessary to clearly distinguish between and use the two. The camera should bounce between ligand view and protein view, and the ligand should appear and disappear.
PyMOL has a powerful and unique molecular movie-making capability. In this next example, the protein is rotated through a full sweep about the Y-axis over frames. Navigation Main page Recent changes Random page Help.
PyMOL Users Manual
Either way, you mkvie provide a prefix which will be used to create numbered PNG files. These image files can then be converted into one movie file. You can do simply supply a number eg. The Motions Mouse Mode is used to store object specific key frames.
If you include an object name, then it stores that object’s position information in the current frame. Why is it so herky-jerky? So, as you can see this is a multidimensional problem: So simple in fact, let’s make a super-quick movie that does exactly what I just mentioned— frames of a slow zoom into some object.
In this exercise we will do a simple ligand dissociation animation. If you want each frame to be ray-traced, you should turn on raytracing of frames, turn off caching, and clear the cache see the Movie Menu or use the following commands. You can also press the mclear button on the external GUI window. An object key frame should automatically be created. There are two ways of mapping states to frames: Converting a sequence of images into a movie can be achieved by many different means depending on the operating system and the available software.
This command tells PyMOL how to assign states to frames.
The mview store tells PyMOL to store the camera or mste coordinates, while the mview reinterpolate command tells PyMOL to link together the saved positions for the camera or the selected object in a smooth, cool way. You can also type: In this exercise we will generate a molecular morph between two conformations of adenylate kinase. The movie panel allows interactive inserting and deleting of frames, as well as moving and copying of key frames.
If we wanted an a zoom in that was pymo, as fast as the zoom out we would simply replace line 16 with.
PyMOL Moviemaking Tutorial
Navigation menu Personal tools Log in. I think it’s help to think of the movie as a set of frames, like in a movie reel, so let’s start there. The following statements create a sixty frame movie which simply rocks the protein by 10 degrees.
Jump to frame mdo and mappend: To change the speed after you have created key frames, you can move key frames or insert additional frames at any given frame. If the mset command is not used, PyMOL will by default play through all states in sequential order. We worry about getting attractive actors first. Trajectory movie In this exercise we create a movie from a trajectory, which is a multi-state object in PyMOL. A free cross-platform converter and editor is provides by the ImageMagick suite of programs thanks to J.
The difference between programs lies in the ease of automation, and the level of control over the creation of image files. Some extra trajectory preparation steps will make this look much more pleasant. Moie sequence of structures from a molecular dynamics simulation gives states.
Each state can be written into an image file, which eventually becomes a movie. So, you can sort of chain the specifications. A frame is a particular orientation, position, and representation of the state.