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).
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 7 (and Vista) 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.
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.
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.
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! Here's how:
At your ConSurf results page, download the PDB file with ConSurf
conservation grades in the temperature field.
At Polyview-3D, under Source of Structural Data,
use the Browse button to upload your ConSurf PDB file.
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.)
Under Advanced Structure Annotation, check Functional
regions from ConSurf.
Click Preview.
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).
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.
(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: 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.