Presenting Molecular Views from
FirstGlance in Jmol

Updated May, 2016.


Quick Start: 

Example Animations.



Complete Details
  1. Static Snapshots
    1. Method 1: FirstGlance Can Save Static Images: Easiest, any size, high quality automatically.
    2. Method 2: Capture A Screenshot.
    3. Method 3: Static Image from Polyview-3D.

  2. Rotating Views
    1. Method 1: FirstGlance Can Save Presentation-Ready Animations.
    2. Method 2: Make A Presentation-Ready Animation with Polyview-3D.
    3. Method 3: Project FirstGlance Itself.
    4. Method 4: Protject Proteopedia.Org.

  3. Browser Compatibility for Saving Images and Animations from FirstGlance.

  4. Troubleshooting Saving Images and Animations from FirstGlance.
    1. Bad (empty) GIF files.
    2. ERROR: capture canceled.
  1. Static Snapshots:   (See below for presenting Rotating Views)

    It is easy to put any molecular view from FirstGlance in Jmol into a presentation or document (Microsoft Powerpoint or Word, Google Slides or Docs, Libre Office).

    1. Method 1: FirstGlance Can Save Static Images.
      • Pros:
        • Easiest method.
        • Automatically saved in high-quality mode regardless of Quality button in FirstGlance.
        • Image defaults to the size of JSmol, but can be set larger (or smaller): 50 to 5,000 pixels.
      • Cons:
        • Does not work in Internet Explorer (which is unacceptably slow and jerky with JSmol anyway).
        • Cannot save when using Java.

      • Method:

    2. Method 2: Capture A Screenshot.
      • Pros:
        • Easy.
        • If you can see the molecule, you can capture an image (from any website, any browser, using Java or not).
        • Works from Proteopedia.Org, where molecular scenes can be customized.
      • Cons:
        • You might forget to depress the Quality button in FirstGlance before capturing.
        • Image cannot be larger than your screen, or smaller than the browser will go.

      • Method:

        1. Use High Quality! Set Jmol to render in high quality:
          • Depress the Quality button (near the Spin button) in FirstGlance in Jmol.
          • In Proteopedia, use the Toggle Quality button below the molecule. Also you may want to use the popup button to make a larger (resizable) image before capture.

        2. MS Windows (7 and later) include a convenient screenshot tool called Snip or Snipping Tool. Click Start, then type snip in the search slot in the Start Menu. The rest is self-explanatory. But here are instructions for Windows 8.

        3. MS Windows XP or earlier: Alt-PrtSc (hold down the Alt key, then press the Print Screen key) copies the active window to the clipboard. You can then paste the image into another application (such as Powerpoint).

          • Cropping an image pasted into MS Powerpoint or MS Word: After you paste the image into an MS Powerpoint slide or MS Word document, click on the pasted image. A "Picture" toolbar will appear. It includes a cropping tool: click on to activate cropping. Edge markers will appear on your pasted image. Drag these to delimit the new cropped image. Click the cropping tool again to de-activate it. Now you can resize the image (with the corner handles) and drag it to the desired position.

        4. Mac OSX:
          • Clipboard: Hold down Command (Apple) plus Shift plus Control (yes, 3 keys all at once!), and then press the "4" key. Now, use your mouse to click and drag a rectangle around what you want to save. When you release the mouse, the image will be saved to the OS X Clipboard. Now you can paste it into Word, Powerpoint, etc.

          • Saving an Image File: Hold down Command (Apple) plus Shift (just 2 keys), and then press the "4" key. Now, use your mouse to click and drag a rectangle around what you want to save. When you release the mouse, the image will be saved directly to a disk file (in Portable Network Graphics or .png format) on your desktop. This file can be displayed in a web browser, inserted into a Powerpoint slide, etc.

    3. Method 3: Static Image from Polyview-3D.
      • Pros:
        • You can customize rendering and coloring.
        • Image will be best publication quality, created by PyMOL.
        • Image can be any size.
      • Cons:
        • Not as easy. Involves learning a new set of controls for rendering and coloring.
        • Many views in FirstGlance are not easily obtained in Polyview-3D (and vice versa).

      • Method: Please see below.



  2. Rotating Views

    1. Method 1: FirstGlance Can Save Presentation-Ready Animations.

      Presentation-ready animations will move in Microsoft Powerpoint, Google Slides, Libre Office, or web pages. (These are multi-GIF files.)

      Here are example slides showing animations saved from FirstGlance:
      Google Slides.
      Download Examples in Powerpoint.

      • Pros:
        • Extremely easy to make from FirstGlance.
        • Can rock back and forth, or spin 360°, around the Y or X axis.
        • FirstGlance can animate customized molecular scenes from Proteopedia.Org. Instructions.
      • Cons:
        • Saving process works in a limited set of browsers. (Once saved, animations work in all browsers and all presentation packages.)
        • May take a few minutes to generate one animation, unless you use Java. Java accelerates the generation of animations by more than ten-fold. Java works in a limited set of browsers.
        • Cannot animate morphs or complex transitions. Can only rock or spin a single molecular scene.

      • Method:


    2. Method 2: Presentation-Ready Animations from Polyview-3D.

      Powerpoint-ready animation made with Polyview-3D. Click animation to ENLARGE.


      See Powerpoint® Examples of Molecular Animations made in PolyView-3D

      • Pros:
        • You can customize rendering and coloring. In contrast, FirstGlance offers a limited set of canned renderings and color schemes.
        • Images are higher quality than images/animations from FirstGlance. This is because Polyview-3D generates images using PyMOL.
        • Morphs can be animated in addition to rocking or spinning. See example in the last slide of the demonstration set linked above.
      • Cons:
        • Involves learning a new interface. You must generate the desired molecular scene using the controls at Polyview-3D. You cannot import a scene from FirstGlance into Polyview-3D.
        • Many views in FirstGlance are not easily obtained in Polyview-3D (and vice versa).
        • Once you submit your animation request to Polyview-3D, you may have to wait an hour (sometimes more) for the file to be generated, especially for larger animations with smooth rotation.

      • Method:
        • Follow instructions at Polyview-3D.
        • After the completed animation appears in the browser, right-click and Save Image As.
        • Drag and drop the saved GIF file into your Powerpoint® slide.

      • ConSurf: Polyview-3D can also make static or rotating views colored from ConSurf results. One slide in the demostration slides linked above shows a protein colored by evolutionary conservation with ConSurf.
        1. At your ConSurf results page, download the PDB file with ConSurf conservation grades in the temperature field.
        2. At Polyview-3D, under Source of Structural Data, use the Choose File button to upload your ConSurf PDB file.
        3. Under Chain Color and Rendering, enter the one-character chain name, and change the color scheme to Conservation. (You will probably also want to set the rendering to spacefill.)
        4. Under Advanced Structure Annotation, check Functional regions from ConSurf.
        5. Click Preview.
        6. You may use the Image Settings (for example to make a larger image) and the Animation Settings (for example to make the molecule rock back and forth in a Powerpoint slide).
        7. Click Submit to obtain your result.

    3. Rotating Views Method 3: Run FirstGlance during your presentation.

      Running FirstGlance during your presentation is a powerful method for including rotatable, molecular views in a presentation. If most of your presentation is in Powerpoint, you would need to pop the FirstGlance browser window in front to show rotating molecular views, then pop Powerpoint back in front afterwards. This method requires a reliable Internet connection when projecting your presentation.

      ConSurf, Pepitope, or Selecton results: Consider downloading your ConSurf/Pepitope/Selecton result so you can guarantee that you have it, even it it gets removed from the server before your presentation. With this method, you can show a ConSurf/Pepitope/Selecton result exactly as it was first shown to you by the server. You will need an Internet connection to upload the saved file into FirstGlance.

    4. Rotating Views Method 4: Proteopedia. At Proteopedia.Org, you can create online customized interactive molecular scenes in Jmol, complete with descriptive text, and green links that display several different molecular scenes. The molecular scenes can be taken directly from FirstGlance in Jmol, following these instructions.

      One big advantage of creating molecular scenes in Proteopedia is that they are immediately online for everyone to see and share. Normal pages in Proteopedia can be edited by anyone (as they can be in Wikipedia). However, you can make protected pages in Proteopedia that only you can change. See Help:Protected Pages.

      Another big advantage of creating molecular scenes in Proteopedia is that they are truly interactive -- they can be rotated and zoomed.

      A third big advantage of showing molecular scenes in Proteopedia is the popup button under every molecular scene. This opens a new, resizable window containing only Jmol with the molecular scene. You can make it as large as you want, then rotate or zoom it.

      ConSurf results can be displayed in Proteopedia as well. On Proteopedia pages titled with a PDB code, click "show" in the blue Evolutionary Conservation bar below the molecule. If you run your own customized ConSurf job, follow these instructions to display your result from a green link in Proteopedia.

      If you prefer to create molecular scenes from scratch within Proteopedia, you can use its built-in Scene Authoring Tools. These are so easy that college students have used them successfully without any training.


  3. Browser Compatibility for Saving Images and Animations with FirstGlance

    The table below concerns only saving graphics. Elsewhere is a more general table about browser compatiblity with FirstGlance.

    • Slower means that generating the animation will take longer than in some other browsers. You will have to wait longer for the animation to be generated, but once completed, it will play at the desired speed.

    • Very Fast means that generating the animation will take less than one-tenth the time that it takes without Java. Playback speed of the completed animation is not affected.

    System Browser
    Save Static Image
    Save Animation
    JSmol (No Java) Jmol Java applet JSmol (No Java) Jmol Java applet
    Windows Internet Explorer Good Good Extremely slow Very Fast!
    Edge Good Java Not Supported Slower but works Java Not Supported
    Chrome Good Java Not Supported Good Java Not Supported
    Firefox Good Good Good Very Fast!
    Opera Good Java Not Supported Does not save Java Not Supported
    Maxthon Good Good Unreliable Very Fast!
    Mac OS X Chrome Good Java Not Supported Slower but works Java Not Supported
    Firefox Good Good Good Very Fast!
    Safari Good Good Good Very Fast!
    Opera Does not work for saving graphics
    Maxthon Does not work for saving graphics

  4. Troubleshooting Saving Images and Animations with FirstGlance.

    1. Bad (empty) GIF files
      Sometimes FirstGlance goes through the motions of generating an animation file, but the GIF file it saves is empty. No image is displayed when such a file is dropped into a browser or a presentation slide. We have seen this problem only in Windows 7 (not in Windows 10), and only when using Java. If you right-click on the saved GIF file and click Properties, the file size is 0 bytes. Successfully saved animations have an icon of the molecular image.
        Empty (zero byte) file icons look like this:
      • Windows 7
      • Windows 10

      Solutions:
      1. Try again. If you try to save the animation several times (no need to restart the browser or anything), you may get lucky.
      2. Use Windows 10. So far we have seen the empty file problem only in Windows 7. You could upgrade to Windows 10, or use a Windows 10 computer if one is available.
      3. Don't use Java. So far, we have never seen the empty GIF file problem when using JSmol (no Java). You will just have to be patient: not using Java slows generation of animations more than ten-fold.


    2. ERROR: capture canceled
      When using Java, if you close all tabs/windows that contain Jmol, then start a new FirstGlance session and attempt to save an animation, you will get "Error: capture canceled". Reloading the only tab/window containing FirstGlance will also induce this problem. Help will appear automatically in FirstGlance that will direct you here.

      You can recover by quitting and re-starting the browser.

      You can avoid this problem by keeping one FirstGlance tab open at all times. It will be best to turn off spinning in this "keeper" tab to avoid loading your computer's CPU. You can open as many FirstGlance sessions as you wish in additional tabs. Closing those tabs won't cause a problem as long as you don't close the "keeper" tab.

      Quitting the browser can be frustrating if you spent some time creating the desired molecular view. It is possible to save the molecular view before quitting the browser. It can be saved as a state script file that contains all information needed to re-create the view. Here are instructions for saving the state script file and re-creating the view.

    Suggestions for clarification or improvements are always welcome.

Feedback to Eric Martz.