When dealing with thousands of frames, it helps to be able to take advantage of multiple cores to do the work. We will set up our trajectory movie with key frames. PNG created by PyMol. Hold down the SHIFT key and drag the ligand out of the binding pocket, using the middle mouse button usually the wheel. In this next example, the protein is rotated through a full sweep about the Y-axis over frames. The “mmatrix” command allows you to store and recall a particular viewing matrix to be used to set up frame 1 of the movie. The following is a Python program with a. There are two ways of mapping states to frames:
Apple provided a nice way to get at the H. PyMOL cannot only animate the camera view, but also the view on individual objects. Report a bug Atlassian News Atlassian. This allows schematic presentation of events like ligand binding or dimer dissociation. Put the following code in a file called. The codec msmpeg4v2 makes movies which are more likely to be playable on standard Windows players and can be used with mencoder e. To change the speed after you have created key frames, you can move key frames or insert additional frames at any given frame.
The “mdo” command allows you to bind a particular series of PyMOL commands to a frame in the movie. 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.
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 “.
Avidemux is a great tool to stich your image files together as a movie.
Navigation menu Personal tools Log in. Once you have rendered frames, there are two steps to encoding a high quality movie.
High Quality Movie Encoding
As an example, if oversized unlabled filenames are of the form. This is most-useful for ray-traced images, but it can also be used with OpenGL images. Camera control with key frames Scene based Movie Independent object motions Timeline editing Trajectory movie Morphing Putting it all together. One approach is to use ImageMagick’s command line interface: The simple approach is to render frames that are between 2x and 3x larger in each direction than the desired final frame, and then average these down to the correct size.
In practice, this is cleaner and more convenient for large scale conversion than the ImageMagick approach. There are two ways of mapping states to frames: Quicktime will spot the pattern and load all other frames in that sequence as well. Store another key frame at or near frame 30 by right clicking on the middle of the movie panel, or type: Independent object motions PyMOL cannot only animate the camera view, but also the view on individual objects. Move or rotate the resolhtion actually: Often it is desirable to have anti-aliased images.
This allows schematic presentation of events like ligand binding or resoltuion dissociation. Scene based Movie This exercise is similar to the previous one, but we will add style information with scenes. This encoder line is however not optimised yetand the codec also produces a bit larger files than the mpeg4 at the same visual quality according to the Mplayer homepage. You don’t need to convert the PyMol scene to a movie, just save session as a. Pyol movie In this exercise we create a movie from a trajectory, which is a multi-state object in PyMOL.
The “mmatrix” command allows you to store and recall a particular viewing matrix to be used to set up frame 1 of the movie.
PNG created by PyMol. Some extra trajectory preparation steps will make this look much more pleasant.
PyMOL Moviemaking Tutorial
Since they are actual python functions, explicit parenthesis are required to invoke them. Note that 2 seconds correspond to 60 framessince the resopution plays with 30 fps frames per second.
Once a movie has been defined, the red “VCR” controls in the lower-right-hand corner of the viewer can be used to step or play through the movie. This generates high quality, yet very large, AVI files; in order to down-size the files into formats which fit PowerPoint, free software such as FormatFactory FF is available for download and easy use.
Go to frame 30, using the movie slider, or by typing: The Motions Mouse Mode is used to store object specific key frames.
Morphing movie using RigiMOL/PyMOL | My software notes
Every state represents a different conformation of the same molecule. Ulead Gif Animator works well although there are many programs to choose from. Gif animation gives a good alternative, retaining the original quality and maintaining small file sizes, however it lacks play controls. Always use object key jovie, never global camera key frames, to store states.
This page talks about how to take your export movie frames and turn them into an actual movie. First, the frames may need some last minute adjustments anti-aliasing, adjusting frame size, applying logos, etc.
When dealing with thousands of frames, it helps to be able to take advantage of multiple cores to do the work.
Report a bug Atlassian News Atlassian. However, if you wish to use the other movie commands such as mdoit is necessary to explicity use the mset pymo to create a movie definition inside of PyMOL. Created by Unknown User schussmalast modified on Mar 27, You can play the movie now.
For free you can use this: A simple Makefile can handle this nicely, regardless of whether one uses ImageMagick or Python Imaging. In this next example, the protein is rotated through a full sweep about the Y-axis over frames.
We will get a multi-state trajectory-like object.
We want to animate how this ligand dissociates from the binding pocket while the protein changes conformation to the open state. Apple provided a nice way to get at the H.
Mencoder can take in various file formats png,gif,jpg and convert them to movies. With skillful use of frame delays during the generation of the Gif it is possible to create pauses to emphasize certain frames.
PyMOL displays a movie panel with a frame slider at the bottom of the pymll. If you load states into an object with a state index of 0, you are indicating that you want the state rwsolution be appended after the last existing state in the object.
By default, each new file loaded will be appended onto the object’s states.