![]() There is currently no menu option to do this, but a small bit of scripting can do the trick. Jmol can create a series of jpg, png, or gif images. 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. Capturing Jmol's renderings as a movie enables much smoother playing rates, e.g. Transparency and large spheres, especially at high quality (set antialiasdisplay on) are some of the renderings that are slow. Jmol may be unable to render large complex animations fast enough to avoid a slow, jerky appearance. There are several possible advantages to true movies. 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. A true movie is a series of images played in sequence. Results may be different for other JSmol websites.This section is about making true movies. The findings below are based primarily on tests with FirstGlance in Jmol in its default HTML5 modality, not using set platformSpeed. FirstGlance in Jmol detects the browser being used, and recommends a different browser when being displayed in Internet Explorer or Opera.In Opera, rotation of the molecule is slow and jerky when setPlatformSpeed is not utilized. Internet Explorer is unacceptably slow (all versions, including version 11). Chrome runs HTML5 best, Safari is good, and Firefox is usually OK (see note under table below). Poor performance in Internet Explorer and Operaĭifferent web browsers have JavaScript engines with different performances. ![]() For registered users who are logged in, Proteopedia has a preference setting that will use Java instead of HTML5. A prominent message is displayed that a simplified model is being shown, and there is a button to load the complete model. Proteopedia loads only amino acid alpha carbon atoms (or nucleic acid phosphorus atoms) and ligand atoms, since its ribbon view (secondary structure schematic) works fine without the other atoms.When using FirstGlance it is recommended that one select Java when the molecule has >20,000 atoms, and especially when there are >50,000 atoms. It offers using the signed Java applet as an option and a preference setting. FirstGlance in Jmol, when using HTML5 (no Java, its default), loads only the first model when there are more than one.Here is how two websites that now use no-Java-JSmol by default have handled these issues: These delays tend to happen with large molecules but are not simply related to model size.) Multiple-model ensembles (such as from NMR experiments) may cause the page to freeze while taking minutes to load the ensemble, or loading may never finish. (FirstGlance, when using HTML5, sometimes freezes for up to a minute, even more. Smaller molecules (20,000 atoms see table at right) may be slow to load and process. ![]() For large systems it is strongly advised to use the set platformSpeed setting (or allow the user to set that). Models with >10,000 atoms are in the largest ~10% of the PDB with >20,000 atoms, the largest ~5% with >50,000 atoms, the largest ~1.5% (counting all models for NMR ensembles).
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