- For Mac it can be downloaded using fink. Mpeg: To convert images to an mpeg movie it is necessary to also install mpeg2encode, which is available from the same places (note, this may be in the 'unstable' branch of fink). To convert a series of numbered ppm files to an mpg movie: convert -delay 6 -quality 95 test.ppm movie.mpg.
- PNG also supports animations with better transparency (try our GIF to APNG). The benefits of using PNG are Plus, PNG is an open format that uses lossless compression. How to open a PNG file? Generally, PNG files will open in your operating system's default image viewer. PNG files are also easily viewable on all web browsers.
- 2Encoding video files
- 2.3Mencoder/Mplayer
- 3Keywords
- 4Movies on a Mac
- 5Troubleshooting
/pathtooverlay.png is the full/relative path to the overlay image 0:v1:v joins the two video streams together, stream 1 is the set of images, stream 2 is the overlay file overlay=0:0 specifies the position of the overlay, in this case the overlay image is assumed to be the same size as the video so no offset is needed. Download MakeAVI for free. MakeAVI is a simple Windows application to assemble a series of JPG (or other formats) images into an AVI file (video). This functionality facilitates making time-lapse movies or stop-motion animations.
Movie Creation in PyMOL
This page talks about how to take your export movie frames and turn them into an actual movie. For learning how to make a movie in the first place, see MovieSchool.
Encoding video files
Animated GIF
Quality note: Converting to video generally leads to a loss of quality and inflated file sizes. Gif animation gives a good alternative, retaining the original quality and maintaining small file sizes, however it lacks play controls. With skillful use of frame delays during the generation of the Gif it is possible to create pauses to emphasize certain frames. Ulead Gif Animator works well although there are many programs to choose from. To create files with many frames in Ulead add around 150 files as frames at a time.
Avidemux
Avidemux is a great tool to stich your image files together as a movie. It can read the PNG output stack from Pymol and encode a movie using almost all codecs currently available. The program has an easy to use graphical interface, making the conversion simple compared to some of the other options available to you.
Open Png File On Mac
Mencoder/Mplayer
Mplayer is an award-winning open source movie player. Mencoder (which comes packaged with Mplayer) is its movie encoder. Mencoder can take in various file formats (png,gif,jpg) and convert them to movies.
Assuming you have created a lot of .png files and would like to encode a .mpeg, .avi or other video format, a number of solutions are known:
- The DiVX encoder using mplayer and mencoder? There's binaries for Unix and Windows. It makes rather nice compression on a 800x600 (probably higher). It doesn't take too long to produce the nicer quailty movies, but much longer than simply
namely something like (this command worked BEST for my case; it's all one line connect it where the backslashes are).
The mpeg4 codec requires a DivX plugin which is not a part of the default installation on some operation systems. The codec msmpeg4v2 makes movies which are more likely to be playable on standard Windows players and can be used with mencoder e.g.
This encoder line is however not optimised (yet), and the codec also produces a bit larger files than the mpeg4 at the same visual quality according to the Mplayer homepage.
Troubleshooting
- If your movie shows up in PowerPoint with only the first frame showing, or is just a black square, try adding -of asf or -of avi.
- If the above line complains about the codec part, then replace the word codec in the command line with vcodec.
Virtual Dub
Virtual Dub is an open-source, robust piece of software that allows easy creation of .AVI files from image sequences (such as *.PNG created by PyMol). After opening Virtual Dub, select File Menu --> Open Video File --> under 'files of type' select image sequence (*.png, etc).
After viewing (and editing) the movie, choose save as AVI (F7) from File menu.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.
Keywords
mencoder, mplayer, movie
Other Options
- For those with Photoshop CS3 installed: Load files using File - Scripts - Load Files into Stack. This loads the files as layers. Turn on the animation window at Window - Animation. You may need to reverse the frames for the correct direction - this is done at the animation window using the drop menu above the frames. You will also want to set a delay on the frames, select all frames using the dropdown menu and and then adjust to 0.2s on one of the frames. Then export the film using File - Export - Render Video. There are plenty of options for format and compression types. I found a quicktime movie with no compression at 10f/s to be right for my needs. The video could get quite big, but it will look as good as pymol. Alternatively you can also create animated GIFs in Photoshop. Once you have the frames of your clip as above, choose File - Save for Web and Devices and then save the GIF. The limit of 200 pictures is a problem in Photoshop.
- Another good program for converting images into movies of different formats is VideoMach : http://gromada.com/VideoMach.html
- TMPGEnc from http://www.tmpgenc.net is very fast, easy to use, and produces very nice ouput (MPEG-2). Unfortunately, it does not handle images larger than 720 x 576 pixels.
- Adobe Premiere recipe, using Microsoft's MPEG4 V2, 960x720 @ 30 fps, which PowerPoint automatically treats as full-screen (due it's wacky metrics). Using this codec, a recent 24-second movie consumed only 4.5 MB of space, but looks much better than a 640x480 Cinepak-based movie with a file size of around ~40 MB. It definitely pays to use the latest technology.
- A freeware jiffy to convert png files to an animation is imgcon, which proved to be very useful:http://www.fmrib.ox.ac.uk/~yongyue/imgcondl.html
- The program convert, part of the ImageMagick suite of programs can be used provided the program mpeg2encode is in your path. mpeg2encode can be found here http://www.mpeg.org/MSSG/. To make an mpeg file, go
If you want to make an animated gif, do
Movies on a Mac
QT Pro
On a Mac, it's easy enough to just fire up QuickTime Player and select
This will prompt you to select the first png file in a folder and load all other pngs with the same base name in that folder. Then simply export these frames as a movie with any of the available quicktime codecs at a frame rate you like.
Alternative
Convert Svg To Png Mac
The above requires QT Pro ($25). For free you can use this: [1].
In a Presentation
You don't need to convert the PyMol scene to a movie, just save session as a .psw (pymol show file) with the scenes embedded in there. Then from within Power|Point just set up a hyperlink (Insert hyperlink) and point it to the .psw file. In presentation mode when you click on the hyperlink pymol automatically boots and you can scroll thru your scens like a full screen powerpoint presentation. You have to make sure that you have pymol installed on your presentation computer (and you have your psw file) and just click OK when powerpoint warns of the perils of non-microsoft products. the final scene will return to your powerpoint presentation without any effort.
Quicktime
Recent attention to transparencies and QuickTime show that one typically wants to set
to tell PyMol to stop using Alpha-channel for transparencies and switch to blending.
If you're having transparency problems this could be a fix.
iOS 11 and macOS High Sierra introduced support for these new, industry-standard media formats:
- HEIF (High Efficiency Image File Format) for photos
- HEVC (High Efficiency Video Coding), also known as H.265, for videos
HEIF and HEVC offer better compression than JPEG and H.264, so they use less storage space on your devices and iCloud Photos, while preserving the same visual quality.
To fully view, edit, or duplicate HEIF and HEVC media on your device, upgrade to the latest version of iOS 11 or later or macOS High Sierra or later. Screen shot en mac.
Capturing this media
When using iOS 11 or later, the following devices can capture media in HEIF or HEVC format. Other devices can view, edit, or duplicate this media with limitations, if using iOS 11 or later or macOS High Sierra or later.
Though capturing in HEIF and HEVC format is recommended, you can set these devices to capture media using the older formats, which are more broadly compatible with other devices and operating systems:
- Go to Settings > Camera.
- Tap Formats.
- Tap Most Compatible. This setting is available only on devices that can capture media in HEIF or HEVC format, and only when using iOS 11 or later.
- All new photos and videos will now use JPEG or H.264 format. To return to using the space-saving HEIF and HEVC formats, choose High Efficiency.
Working with this media
Support for HEIF and HEVC is built into iOS 11 and later and macOS High Sierra and later, letting you view, edit, or duplicate this media in a variety of apps, including Photos, iMovie, and QuickTime Player.
On some older devices, support for HEVC is affected by the resolution and frame rate (fps) of the video. Resolutions of 1080p or lower and frame rates of 60 fps or lower are more broadly compatible with older devices. To reduce the resolution and frame rate that your capture device uses for recording video, go to Settings > Camera > Record Video, as well as Settings > Camera > Record Slo-mo.
If you're using iCloud Photos with iOS 10 or macOS Sierra, you might see a warning icon in the upper-right corner of the photo or video, or you might see an alert message. To fully view, edit, or duplicate HEIF and HEVC media on your device, upgrade to iOS 11 or later or macOS High Sierra or later.
Sharing this media
QT Pro
On a Mac, it's easy enough to just fire up QuickTime Player and select
This will prompt you to select the first png file in a folder and load all other pngs with the same base name in that folder. Then simply export these frames as a movie with any of the available quicktime codecs at a frame rate you like.
Alternative
Convert Svg To Png Mac
The above requires QT Pro ($25). For free you can use this: [1].
In a Presentation
You don't need to convert the PyMol scene to a movie, just save session as a .psw (pymol show file) with the scenes embedded in there. Then from within Power|Point just set up a hyperlink (Insert hyperlink) and point it to the .psw file. In presentation mode when you click on the hyperlink pymol automatically boots and you can scroll thru your scens like a full screen powerpoint presentation. You have to make sure that you have pymol installed on your presentation computer (and you have your psw file) and just click OK when powerpoint warns of the perils of non-microsoft products. the final scene will return to your powerpoint presentation without any effort.
Quicktime
Recent attention to transparencies and QuickTime show that one typically wants to set
to tell PyMol to stop using Alpha-channel for transparencies and switch to blending.
If you're having transparency problems this could be a fix.
iOS 11 and macOS High Sierra introduced support for these new, industry-standard media formats:
- HEIF (High Efficiency Image File Format) for photos
- HEVC (High Efficiency Video Coding), also known as H.265, for videos
HEIF and HEVC offer better compression than JPEG and H.264, so they use less storage space on your devices and iCloud Photos, while preserving the same visual quality.
To fully view, edit, or duplicate HEIF and HEVC media on your device, upgrade to the latest version of iOS 11 or later or macOS High Sierra or later. Screen shot en mac.
Capturing this media
When using iOS 11 or later, the following devices can capture media in HEIF or HEVC format. Other devices can view, edit, or duplicate this media with limitations, if using iOS 11 or later or macOS High Sierra or later.
Though capturing in HEIF and HEVC format is recommended, you can set these devices to capture media using the older formats, which are more broadly compatible with other devices and operating systems:
- Go to Settings > Camera.
- Tap Formats.
- Tap Most Compatible. This setting is available only on devices that can capture media in HEIF or HEVC format, and only when using iOS 11 or later.
- All new photos and videos will now use JPEG or H.264 format. To return to using the space-saving HEIF and HEVC formats, choose High Efficiency.
Working with this media
Support for HEIF and HEVC is built into iOS 11 and later and macOS High Sierra and later, letting you view, edit, or duplicate this media in a variety of apps, including Photos, iMovie, and QuickTime Player.
On some older devices, support for HEVC is affected by the resolution and frame rate (fps) of the video. Resolutions of 1080p or lower and frame rates of 60 fps or lower are more broadly compatible with older devices. To reduce the resolution and frame rate that your capture device uses for recording video, go to Settings > Camera > Record Video, as well as Settings > Camera > Record Slo-mo.
If you're using iCloud Photos with iOS 10 or macOS Sierra, you might see a warning icon in the upper-right corner of the photo or video, or you might see an alert message. To fully view, edit, or duplicate HEIF and HEVC media on your device, upgrade to iOS 11 or later or macOS High Sierra or later.
Sharing this media
iCloud Photos preserves media in its original format, resolution, and frame rate. If your device can't fully view, edit, or duplicate HEIF or HEVC media in iCloud Photos, or displays it at a lower resolution, upgrade to iOS 11 or later or macOS High Sierra or later.
When you share media using other methods, such as AirDrop, Messages, or email, it might be shared in a more compatible format, such as JPEG or H.264, depending on whether the receiving device supports the newer media format.
Converting this media
You can convert HEIF and HEVC media by exporting to a different format from an Apple or third-party app. For example:
- If you open an HEIF image in Photos or Preview on your Mac, you can choose File > Export, then choose a format such as JPEG or PNG before saving.
- If you open an HEVC video in QuickTime Player on your Mac, you can choose File > Export As, then save to H.264 by making sure the HEVC checkbox isn't selected.
Little Mac Png
Importing this media via USB
When you import HEIF or HEVC media from an attached iOS device to Photos, Image Capture, or a PC, the media might be converted to JPEG or H.264.
You can change this import behavior in iOS 11 or later. Go to Settings > Photos. In the TRANSFER TO MAC OR PC section, tap Keep Originals to prevent the media from being converted to JPEG or H.264 when importing.
