BIOC351: Proteins. PyMOL Laboratory #4. Movie Making

Transcription

1 BIOC351: Proteins PyMOL Laboratory #4 Movie Making Version 2 Some information and figures for this handout were obtained from the following sources: Moviemaking in PyMOL (2009 DeLano Scientific LLC)

2 There are times that static images just can t relate the story that you are trying to convey to your audience. This is when you can harness the power of the PyMOL movie making tools. With recent advancements in the PyMOL code base, the movie making tools have grown exponentially. Today we ll first focus on making movies using the pull down menus and end with generating movie scripts Movie Terminology In PyMOL a state corresponds to a given three-dimensional representation of your object(s). For example, a rotating or translating molecule is one state, regardless of its orientation or position. A sequence of 20 structures from a NMR structure generates 20 states. A frame is a particular orientation, position, and representation of the state. Frames can be written into an image file, which when linked together become a movie. The user defines the order of scenes in a show. PyMOL creates a smooth transition between camera motions in the various scenes. Camera Motions PyMOL defines three types of camera motions: 1. Roll the object(s) will smoothly roll through X degrees in Y seconds 2. Rock the objects(s) will rock back and forth X degrees in Y seconds 3. Nutate the object(s) will roll through 2 axes by X degrees and pause in Y seconds Exercise A: Let s start today s exercise using Monday s Exercise-A.pml script. To run this script, select File à Run from the Menu bar and find the script you modified for Exercise-A.pml. BIOC 351: Proteins 2

3 2014 Try the different camera motions by selecting Movie à Program à Camera Loop à (Nutate/Rock/Roll). To play the movie you have two choices click on the Play button in the Upper Control panel or click on the > in the movie control panel (see orange circles). Between trials remember to reset the movie controls with Movie à Reset or you will have trouble deducing the actions of your commands. Scenes A scene represents the object(s) in all its final form. It maybe a distance shot of a cartoon representation of your structure or it might be highlighting the hydrogen bonding pattern of a ligand binding. In recent versions of PyMOL they have introduced a mechanism to link static scenes together. This is accomplished by having PyMOL interpolate a trajectory for the camera to smoothly transition between two scenes. Let s see how this works: Click Scene à Buttons (this places a check by it when you return) Turn off all you objects except 1h76 & fe by clicking on them. Orient pig so it fills your screen. Click Scene à Append. Note that if a grey box does not appear in the lower left corner of your viewing window that says 001 Movie controls. retoggle Scene à Buttons off and the on. Right click on it and select rename. This places a box at the top of your viewing window where you can change the name. I suggest something like: fullview BIOC 351: Proteins 3

4 2014 Now turn on an object (carbonate, sugar, ligands, all) and move the scene around zoom up, slab it to focus the viewers attention on your new object. Click Scene à Append. Note that a new grey box appears below your named scene with 001 right click and rename it. To generate a third scene I suggest putting a surface on you could make an electrostatic surface, your could just make a semi transparent surface your choice. Click Scene à Append again and rename it surface. You can see how you could walk through your objects highlighting all of the important features in this manner. However lets walk through and see what you have done. This can be accomplished by clicking on the names of the scenes you have created. To get PyMOL to link the scenes together lets use: Movie à Program à Scene Loop à Nutate à 8 seconds each This tells PyMOL that once it has animated to your scene, roll it around for 8 seconds before translating to your next scene. To see your movie just click the Play button in the Upper Controls or click the > in the movie control box. Before we actually create a movie it is ALWAYS wise to save your session file so if PyMOL crashes you haven t lost everything. File à Save Session To make a movie, just click File à Save Movie As On a PC you need to use MPEG, but on a Mac I recommend Quicktime. You will notice that in your information box lots of things appear when its done you should see the word finish. Now the image quality of your movie isn t great because we didn t Ray trace the image (Movie à Ray Trace Frames). I usually only do this when I really like my movie or you can spend hours waiting for something that you will throw away! Timelines If you look at the bottom of the window you will see a timeline has appeared: Movie timeline. BIOC 351: Proteins 4

5 Clicking on the timeline with your middle mouse key places at that specific frame. The 2014 Adjusted movie timeline. blue boxes are known as key frames frames in which the object or camera are undergo a change. Note each box (key frame) is a single frame. The timeline can be adjusted: Control Left click drag right adds time. Control Left click drag left deletes time. If you forget a scene you can insert it into the timeline. Click on the scene in which you want the new scene to appear before. Generate a new scene perhaps display hydrogen bonds, show waters (create waters, resn hoh), or display as b factor putty (A à preset à b factor putty). Scene à Insert Before and rename your scene. You can either click on the scene and select a motion for it from Movie à Program à Scene Loop à your favorite motion OR you can reset everything (Movie à Reset) and then select the same motion for everything like before: Movie à Program à Scene Loop à Nutate à 8 seconds each Moving Objects So far all we have really done is just rotated objects around and zoomed in or out. Let s now add some real movement to our movies. We will be using an exercise created for the Moviemaking in PyMOL guide. Please down load the following files from : Dimer_script.pml 3f9f.pdb Run dimer_script.pml what are you looking at? Open in the script in your text editor to see what is being displayed. Let s first start with creating the dimer. To do that we will be dragging Chain A away from Chain B. To do that you first must put your mouse in motion mode: Mouse à 3 Button Motions Next we need to store the original position of Chain A to do that Click on the M beside Chain A and select Store. BIOC 351: Proteins 5

6 Now move the movie slider to frame 90 (look above the movie controls at the lower left to see the frame you are on) To prepare to move, click on the Chain A M à drag Now hold your shift key and the middle mouse key and move chain A somewhere. Dragging controls in the Objects window. When you are done click in on Done in the Objects window. Click play so see what your movie would appear like. Let s add some rotations to our movement. First lets clear the rotations that we have move the slider to frame 90. Select Chain A M à clear Again, store your state Chain A M à store followed by M à drag Now this time use shift-left mouse button to rotate Chain A as well as shift-middle button to move. Click done when you are happy and play it. Exercise B: Let s take this script you have been making and combine it with what we learned with Scenes. I suggest having the dimer open up to expose the surface that is holding them together perhaps it is electrostatic?! BIOC 351: Proteins 6