Creating Movies - Revision history

EricMartz at 22:00, 3 January 2021

2021-01-03T22:00:00Z

Fuse809: /* Windows */ Adding in two ways I've discovered of doing this in Windows.

2014-05-01T20:22:47Z

‎Windows: Adding in two ways I've discovered of doing this in Windows.

NicolasVervelle: /* Encoding to the mpeg format */ https://sourceforge.net/tracker/?func=detail&aid=3517513&group_id=23629&atid=379133

2012-05-28T15:18:55Z

‎Encoding to the mpeg format: https://sourceforge.net/tracker/?func=detail&aid=3517513&group_id=23629&atid=379133

EricMartz: /* Example I */

2012-01-14T02:23:55Z

‎Example I

EricMartz at 02:22, 14 January 2012

2012-01-14T02:22:35Z

EricMartz: /* Movies from trajectories */

2012-01-14T02:11:57Z

‎Movies from trajectories

EricMartz: /* Linux */

2012-01-14T02:11:20Z

‎Linux

EricMartz: /* Creating images */

2012-01-14T02:08:41Z

‎Creating images

EricMartz: /* Images from script, Example II (e.g. in pre-11.7 Jmol) */

2012-01-14T02:07:45Z

‎Images from script, Example II (e.g. in pre-11.7 Jmol)

EricMartz: /* Alternative approach (e.g. in pre-11.7 Jmol) */

2012-01-14T02:00:56Z

‎Alternative approach (e.g. in pre-11.7 Jmol)

← Older revision		Revision as of 22:00, 3 January 2021
Line 6:		Line 6:

	Jmol can create a series of jpg, png, or gif images. There is currently no menu option to do this, but a small bit of scripting can do the trick. It is possible to get the movie output from either one frame at several angles or from a series of frames. The images can then be assembled into a single file that will play as a movie.		Jmol can create a series of jpg, png, or gif images. There is currently no menu option to do this, but a small bit of scripting can do the trick. It is possible to get the movie output from either one frame at several angles or from a series of frames. The images can then be assembled into a single file that will play as a movie.
		+
		+	=Animations Quickly & Easily=
		+	*FirstGlance: Any molecular scene you get in [http://firstglance.jmol.org FirstGlance in Jmol] (no Jmol commands needed!) can be saved, rocking or spinning, as a presentation (slide) ready movie (GIF file) with just a few clicks of the mouse. [http://firstglance.jmol.org/slides.htm Instructions].
		+	*Any molecular scene you obtain in Jmol can bs saved, rocking or spinning, as a presentation (slide) ready movie (GIF file) using the FirstGlance [https://proteopedia.org/wiki/fgij/animation_kit_instructions.pdf Animation Kit].

	=Image/Movie Size=		=Image/Movie Size=

@@ Line 216: / Line 216: @@
 ==Windows==
-(Someone with experience on Windows is needed to write this section. It is possible that Quicktime Pro will work on Windows as it does on Mac OS X.)
+In PhotoScape one needs to open the '''Animated GIF''' tab, then click '''Add''' and select all the images one wishes to animate. Then, using the '''Change time''' option animate your image files and when you are complete click "Save" to save your work.
 ==Linux==

@@ Line 231: / Line 231: @@
 Alternatively, encode to smaller <code>mpeg4</code> files with <code>mencoder</code>, which comes along with <code>mplayer</code>.
-Many options and codecs are available, the default settings often create images that are too grainy due to the high image compression. Some testing by Mario Valle at CSCS gave [http://personal.cscs.ch/~mvalle/mencoder/experiment.html optimal mencoder options] for a movie of atomistic simulations. To have it run on default Windows installations (e.g. for use in Powerpoint), also use the [http://lists.mplayerhq.hu/pipermail/mencoder-users/2006-September/004130.html msmpeg4v2 codec with autoaspect]. The optimal combination of mencoder options then becomes:
+Many options and codecs are available, the default settings often create images that are too grainy due to the high image compression. Some testing by Mario Valle at CSCS gave [http://mariovalle.name/mencoder/experiment.html optimal mencoder options] for a movie of atomistic simulations. To have it run on default Windows installations (e.g. for use in Powerpoint), also use the [http://lists.mplayerhq.hu/pipermail/mencoder-users/2006-September/004130.html msmpeg4v2 codec with autoaspect]. The optimal combination of mencoder options then becomes:
 <pre>

@@ Line 40: / Line 40: @@
 = Images from a script =
 ==Example I==
-Here is a loop that will generate a series of jpg images for a 360 degree rotation in 1 degree increments. The jpg files are named m1.jpg, m2.jpg, ..., m360.jpg. See the section below on Windows Media format for further explanation of the "extra frames".
+Here is a loop that will generate a series of jpg images for a 360 degree rotation in 1 degree increments. The jpg files are named m1.jpg, m2.jpg, ..., m360.jpg. This script fragment does not include the commands needed to color, render and orient the molecule as you wish. See below for more on that. See the section below on Windows Media format for further explanation of the "extra frames".
 <pre>
 # goal: a 360 degree spin

@@ Line 3: / Line 3: @@
 This section is about making true movies. A true movie is a series of images played in sequence. Unlike a "live" animation in Jmol, if all you have is the movie, you cannot use the mouse to rotate the molecule to watch the movie from different perspectives, nor can you change the color scheme or rendering of the molecule.
-There are several possible advantages to true movies. Jmol may be unable to render large complex animations fast enough to avoid a slow, jerky appearance. Transparency and large spheres, especially at high quality (set antialiasdisplay on) are some of the renderings that are slow. Capturing Jmol's renderings as a movie enables much faster playing, e.g. 24 frames per second. Another advantage is that the movie can be shared as a single file, and kept private, in situations where one does not want the animation on a public website, and when the recipient is not familiar with using the stand-alone Jmol application.
+There are several possible advantages to true movies. Jmol may be unable to render large complex animations fast enough to avoid a slow, jerky appearance. Transparency and large spheres, especially at high quality (set antialiasdisplay on) are some of the renderings that are slow. Capturing Jmol's renderings as a movie enables much smoother playing rates, e.g. 24 frames per second. Another advantage is that the movie can be shared as a single file, and kept private, in situations where one does not want the animation on a public website, and when the recipient is not familiar with using the stand-alone Jmol application.
 Jmol can create a series of jpg, png, or gif images. There is currently no menu option to do this, but a small bit of scripting can do the trick. It is possible to get the movie output from either one frame at several angles or from a series of frames. The images can then be assembled into a single file that will play as a movie.

@@ Line 10: / Line 10: @@
 Normally you simply adjust the size of the Jmol application window to the desired size before writing the image files. If you want an exact size, such as 640 x 480 pixels, you can set that easily. Open Jmol's ''Display'' menu and select ''Resize''. If you want an image larger than you can achieve by resizing your window using a mouse, it can be set using the ''Display, Resize'' method. You may not be able to see the entire Jmol window on your screen if you set a large size, but the images will be saved at the desired size (for example 1024 x 768 pixels).
-= Movies from trajectories =
+= Images from trajectories =
 == Trajectories read in as multiple files ==

@@ Line 214: / Line 214: @@
 ** Restrict profiles to: Main
 ** Encoding mode: Best quality (multi-pass)
 ==Linux==
@@ Line 239: / Line 243: @@
 </pre>
 Fine tune the speed/length of the animation by varying the -fps (frames per second) option.
 == Encoding to animated gif format ==

← Older revision		Revision as of 02:08, 14 January 2012
Line 144:		Line 144:


−	== Creating images ==	+	== Creating images (linux) ==

	* Linux console:		* Linux console:

@@ Line 38: / Line 38: @@
    script "trajectorymovie.jmol"
-= Images from script, Example II (e.g. in pre-11.7 Jmol) =
+= Images from a script =
 The main part of the script is given here: [http://sourceforge.net/mailarchive/message.php?msg_id=46C4DE84.9050805%40stolaf.edu based on a mail from Bob Hanson on the mailing list]. If you want to rotate a single molecule, you need to uncomment the respective 'rotate' commands. If you want to loop over the timeframes in your coordinate file, you only need to change the 'nFrames' variable to the amount of frames you are currently using (this is given in the title of the main Jmol window).

@@ Line 38: / Line 38: @@
    script "trajectorymovie.jmol"
-= Alternative approach (e.g. in pre-11.7 Jmol) =
+= Images from script, Example II (e.g. in pre-11.7 Jmol) =
 The main part of the script is given here: [http://sourceforge.net/mailarchive/message.php?msg_id=46C4DE84.9050805%40stolaf.edu based on a mail from Bob Hanson on the mailing list]. If you want to rotate a single molecule, you need to uncomment the respective 'rotate' commands. If you want to loop over the timeframes in your coordinate file, you only need to change the 'nFrames' variable to the amount of frames you are currently using (this is given in the title of the main Jmol window).
@@ Line 68: / Line 68: @@
 Save this text in a file, for example 'movieloop.jmol'.
-== Alternative example ==
+== Example III ==
 This uses the same principles, slightly different (though equivalent) code and is set for the rotation of the model in a single frame. In addition, it exports to <code>gif</code> format (only available in recent 11.7 versions) for later making an animated <code>gif</code> file outside Jmol:
@@ Line 127: / Line 127: @@
 Jmol will start, and show you the animation, while it is writing the output files.
 = Converting images to a playable movie =