We will get a multi-state trajectory-like object. 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. PyMOL has a powerful and unique molecular movie-making capability. In order to use it, you first need to understand a few key concepts:. If the mset command is not used, PyMOL will by default play through all states in sequential order. Storing commands with frames mpng and movie.
You can play the movie now. An extra M button should appear for every object in the object menu panel. With the morph from the previous exercise we will create a movie which combines camera, object motions, and state transitions. This gives a global 1: The “mdo” command allows you to bind a particular series of PyMOL commands to a frame in the movie. Trajectory movie In this exercise we create a movie from a trajectory, which is a multi-state object in PyMOL. 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. However, if you wish to use the other movie commands such as mdo , it is necessary to explicity use the mset command to create a movie definition inside of PyMOL.
Fetch PDB 1t46 or load it from https: 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. You can save movie images to numbered PNG format files with a common prefix. See “help load” or consult scrlpt reference section for more information.
PyMOL displays a movie panel with a frame slider at the bottom of the window. Timeline editing The speed of interpolations depends on the number of frames between two key frames. You can save the movie using the “mpng” command, or you can save it from the “File” menu.
An extra M button should appear for every object in the object menu panel. The “mmatrix” command allows you to store and recall a particular viewing matrix to be used to set up frame 1 of the movie.
Every state represents a different conformation of the same molecule. Note that 2 seconds correspond to 60 framessince the movie plays with 30 fps frames per second. Scene based Movie This exercise is similar to the previous one, but we will add style information with scenes. In this exercise we will generate a molecular morph between two conformations of adenylate kinase. The “load” command is used to populate states of an object. An object key frame should automatically be created.
Independent object motions PyMOL cannot only animate the camera view, but also the view on individual objects. PyMOL has a powerful and unique molecular movie-making capability.
Don’t close PyMOL but continue with the last exercise. You can also press the mclear button on the external GUI window. If you are compressing movies using Adobe Premiere recommended for best qualityyou will probably want to convert the files using ImageMagick or a similar package into a format that Premiere is capable of reading such as “. 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.
Relevant commands for scripting mset and madd: You can also type: 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. Some extra trajectory preparation steps will make this look much more pleasant.
The mset command is followed by an arbitrarily list of statements which defines the entire movie. We want to animate how this ligand dissociates from the binding pocket while the protein changes conformation to the open state.
If you want each frame to be ray-traced, you should turn on raytracing of frames, turn off caching, and clear the cache see scfipt Movie Menu or use the following commands.
Camera control with key frames Scene based Movie Independent object motions Timeline editing Trajectory movie Morphing Putting it all together.
However, the optional third argument to the load command is the frame index into which the file should be loaded. See “help mmatrix” or the reference section for more information. Since they are actual python functions, explicit parenthesis are required to invoke them. Either way, you must provide a prefix which will be used to create numbered PNG files. This is more flexible, it allows us to control the mapping per object and do non Go to frame 30, using the movie slider, or by typing: The speed of interpolations depends on the number of frames between two key frames.
There are two ways of mapping states to frames: PyMOL has the ability to cache a series of images in RAM scriph to play them back at a much higher rate than they could be rendered originally.
PyMOL Users Manual
It will look very jittery. However, if you wish to use the other movie commands such as mdoit is necessary to explicity use the mset command to create a movie definition inside of PyMOL.
Store another key frame at or near frame 30 by right clicking on the middle of the movie panel, or type: