Presenting Views from FirstGlance

Presenting Molecular Views from
FirstGlance in Jmol

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 Open Office Impress or Writer).
- MS Windows: 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.
  - To avoid the need for cropping, it is convenient to "lasso" the desired graphic with the mouse when saving it. MS Windows XP does not provide any built-in method to lasso the desired portion of the screen (instead of copying the entire active window, and then cropping the image), but an inexpensive program called PrintKey is excellent for this.
- 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.
Polyview-3D can make 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. However, it is not taking 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!
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. (In contrast to FirstGlance, you can run Protein Explorer off-line using a downloaded copy.)

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. (You can show ConSurf but not Pepitope or Selecton files off-line using a downloaded installation of Protein Explorer).
Rotating Views Method III: MolSlides.
1. MolSlides can use Jmol, enabling them to display on all popular computer platforms and browsers. However, creating the MolSlides in the first place requires using Protein Explorer (PE), which works only in MS Windows.
2. MolSlides are ideal when you don't need the control panel or other capabilities of FirstGlance, but simply a few pre-selected, rotatable molecular views in a set of slides. Making MolSlides takes more effort than method I above, because you have to learn how to use Protein Explorer. Once you have made your MolSlides, you can show them (off-line or on-line) without having to run PE, using Jmol. Here is a sample of ConSurf views saved as MolSlides using Jmol. (Because Protein Explorer cannot display Pepitope nor Selecton results, making Pepitope/Selecton MolSlides is not straightforward.)
3. A MolSlide can be inserted into a Powerpoint slide (Windows only), but this is technically fussy. (For more information, please see molslides.proteinexplorer.org.) Usually it is far easier to run your MolSlides in a browser window, and pop it in front of Powerpoint when you want to show your rotating molecular views. You can then resume Powerpoint by popping it in front of the MolSlides browser window.
4. For ConSurf results, you are not limited to presenting the preset molecular views produced by ConSurf. Instructions for customizing the molecular view within PE are linked at the bottom of ConSurf's control panel, "Customize this molecular view -- Explore this structure". You can save any molecular view that you obtain in PE into a MolSlide.
5. Briefly, to save molecular views for later presentation as MolSlides: Run Protein Explorer, get the molecular view you want, then find the link Save This View .. below PE's message box. Click it, and in the dialog that opens, click Add a new MolSlide. Follow instructions there. Full details and more examples are at molslides.proteinexplorer.org.

Feedback to Eric Martz.