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. Navigation Main page Recent changes Random page Help. The syntax for mset can be a little tricky at first. Let’s look at the inhibitor complex again, pdb 1TE1. Navigation Main page Recent changes Random page Help. Now the we have the appropriate terminology to talk about movies in PyMOL, we can discuss what a movie really is.
This page was last edited on 4 December , at This command has a similar idea of frame , but works a little differently. This will make sense with an example. Once this is done we can reinterpolate through scenes to have beautifully smooth transitions. Now that we’re experts at moving the PyMOL camera around, let’s start moving objects around while keeping the camera steady. To change the speed after you have created key frames, you can move key frames or insert additional frames at any given frame. So, now you see why it’s necessary to clearly distinguish between and use the two. Line 23 assigns scene to frame
Retrieved from ” http: We just connected the two scenes and asked PyMOL to make the transition between the two smooth. We will set up our trajectory movie with key frames.
MovieSchool 4 – PyMOLWiki
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. Line 23 assigns scene to frame An object key frame should automatically be created.
We need two objects: This time, we would like to make a more compex movie that shows moving objects not the camera and changing representations. One of our first movies above was a very simple zom on an atom in an amino acid. Independent object motions PyMOL cannot only animate the kovie view, but also the view on individual objects. In line 19, we save this new camera position and the sticks representation of TRP in the scene called Line 5 makes a 90 frame movie that only spans the first state.
If you’re not yet at this level, please check out the Tutorial Category of pages most notably the beginner tutorials. Go to frame 30, using the movie slider, or by typing: In PyMOL, to attach a scene to a frame or, technically a frame to a scene we simply do the following:.
If you don’t want to rotate all the way around, use this.
MovieSchool 5 – PyMOLWiki
We start simple and build up the complexity. A extract BBc. So, now you see why it’s necessary to clearly distinguish between and use the two.
Lines 1—2 set PyMOL up to show you scene buttons and the movie panel. The mview store tells PyMOL to store mofie camera or objects coordinates, while the mview reinterpolate command tells PyMOL to link together the saved positions for the camera or the pymo object in a smooth, cool way.
This exercise is similar to the previous one, but we will add style information with scenes. Let’s start by defining a few PyMOL concepts—states, frames and scenes.
Zom 1akeA structure has a bound ligand. Relevant commands for scripting mset and madd: This page was last edited on 15 Octoberat Now let’s combine the above two sections into one movie that has both object and camera motions. So, as you can see this is a multidimensional problem: Somewhere zoo, then and issuing mplay PyMOL created 20 frames for your object and assigned one state to each frame. As you know mplay just plays the movie.
PyMOL cannot only animate the camera view, but also the view on individual objects. This is the idea of camera motions in PyMOL. In line 14 we actually make the scene-to-frame assignment with the mview store command, specifying the mapping between scene and frame 1.
One for the protein, and one for the ligand. The movie panel allows interactive inserting and deleting of frames, as well as moving and copying of key frames.
The Motions Mouse Mode is used to store object specific key frames. Let’s look at the inhibitor complex again, pdb 1TE1. Since both molecules will be in the same object after loading 1t This created the animated effect as we scroll through the frames. Every state represents a different conformation of the same molecule. Trajectory movie In this exercise we create a movie from a trajectory, which is a multi-state object in PyMOL.
I would write the syntax as:. This little page will provide the necessary ideas, links, code and examples for making movies in PyMOL. Well, we never gave PyMOL any number of frames to interpolate the change from frame back to frame 1 since it wraps.
Using pymoo as you can see from above is pretty simple. You can play the movie now. Views Read View source View history. Type help mset in PyMOL for more info or see mset.
Some extra trajectory preparation steps will make this look much more pleasant. Lines 17 and 18 change the representation from lines to sticks and then orients the TRP residue which causes the camera to move. The first ‘scene’ was the entire amino acid py,ol the 2nd ‘scene’ was the zoomed in atom.
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