Presenting Molecular Views from
FirstGlance in Jmol
Updated 2010, 2016.

- Static Snapshots: (See below for presenting Rotating Views)
  It is easy to copy any molecular view from FirstGlance in Jmol, and then paste it into a presentation or document (such as into MS Powerpoint, MS Word, or the free presentation or document editing programs within Open Office).
  - 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.
  - 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.
  - 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.
  - 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 a Powerpoint slide.
    - 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.
  Proteopedia.Org can make customized static molecule scenes at high quality -- see also below. You can use the popup button to enlarge your scene to nearly full screen before capture (resize the popup window). Be sure to toggle quality to high quality before popping the image up to large size.
  Polyview-3D can make truly publication quality static views -- see below.

- Rotating Views:
- Rotating Views Method I: Use Polyview-3D

  Powerpoint-ready animation made with Polyview-3D.

  This is by far the easiest and best way to put a rotating molecular view in a Powerpoint® slide.

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

  This method does not take the view from FirstGlance in Jmol -- you generate the view by filling out a simple form (with great flexibility for rendering, coloring, hiding) at Polyview-3D. You can also make static views here, and even animations of morphs.
  Once Polyview-3D has generated your image (large, smoothly-animated images may take up to an hour to make), you simply drag and drop it into your Powerpoint® slide!
  Polyview-3D can also make static or rotating views colored from ConSurf results! Here's how:
  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 see your result.
- Rotating Views Method II: 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 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 show the saved file in FirstGlance.
- Rotating Views Method III: 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.

Feedback to Eric Martz.