Capturing Videos from
FirstGlance in Jmol
New in August, 2023 (FirstGlance version 4.2).

FirstGlance has built-in methods for making a rocking or spinning animation of any of its molecular views. If that is what you want, go to Presenting Views from FirstGlance.


Capsid of Eastern Equine Encephalitis Virus (6mx4, automatically simplified by FirstGlance to every 10th alpha carbon). Solid views by FirstGlance, in order:
  1. Closest to center and farthest from center (initial default).
  2. ✓ Slab (Views tab).
  3. Slab: ✓ Don't hide the back, ✓ Rotate slab (half capsid).
  4. Solid (Views tab), Distinct colors for each group of sequence-identical chains: E1, E2, Capsid.
  5. Slab off.
(MP4 file.)
Two confirmations 1, 2 of several sidechains in 7rin. Automatic animation by FirstGlance. (GIF file.)
Same perspective of 7rin as above, but rendered as the Charge view: +, —. Automatic animation of conformations (alternate locations) by FirstGlance. (GIF file.)
Auto zoom-in and labeling by FirstGlance of the isopeptide bond in 2xi9 (Tools tab, Protein Crosslinks), followed by manual slabbing, rotation with the mouse, and further zooming. (MP4 file.)
This document tells you how to capture more complex videos from FirstGlance (or Proteopedia.Org, or any video displayed on your computer screen). These can be video sequences generated automatically by FirstGlance (such as zooming in to an isopeptide bond protein crosslink in 2xi9), or manually controlled sequences of operations. Examples are at the right.

  1. Capture the Video

    1. Windows 11. The Snipping Tool included in Windows 11 build number 22621.1344 or higher can capture videos as MP4 files. You can limit capture to a rectangle that you size within your screen. Use the Windows Search slot to find "Snipping". If you need help, search the Internet for "screen record with snipping tool".

    2. Windows 10 does not have a built-in video capture tool. Upgrade to Windows 11 is free if your computer meets the minimum requirements. A free video capture tool that some people recommend for Windows 10 can be downloaded from obsproject.com.

    3. macOS 10.14 (Mojave) or later include a Screenshot Toolbar that can record video within a rectangle that you size within your screen. Shift + Cmd + 5 invokes it. It saves videos as MOV files.

    If you have recorded a long (15 sec or more) sequence that you want to play once from start to finish, you are all set (unless you need to cut out some unwanted segments ... see below). MOV and MP4 files play in slides in Powerpoint and other presentation software, as well as within websites in common browsers. If an MOV file does not play, try converting it to an MP4 file (see below).

  2. Convert the Video

    1. Convert MOV to MP4. A free conversion site with many options is cloudconvert.com. Drag your captured video file and drop it into cloudconvert.com.

      MP4 files are more widely supported than are MOV files. Also, if you captured an MOV on macOS, sometimes it has an unwanted artifact, a green edge on the right side. That can be cropped off during conversion by specifying a custom resolution (width and height in pixels) and changing Fit to crop. Similarly, you can reduce the overall size.

      Get the pixel dimensions of a video on macOS with Cmd-I (Get Info). On Windows, right click the file and select Properties. The dimensions will be reported under the Details or Summary tab. (If you have better methods for Windows, please email us using the link at the bottom of this page.)

    2. Convert to GIF. If you want a short video clip (15 sec or less) to loop, playing over and over repeatedly, convert it to a GIF file.

      You may want to run it through cloudconvert.com first, even MP4 to MP4, because you can make various adjustments that are not available in the conversion to GIF step. Changing frames per second (Fps) to about 10 seems to result in a faster playback after the subsequent conversion to GIF.

      Finally, convert to GIF. The GIF option is under Image (not Video), but nevertheless it creates a movie when starting with an MP4 or MOV movie.

  3. Cut Out Unwanted Segments.

    LosslessCut is a free program that makes it easy to cut out unwanted portions of the video, merging the remaining segments. Lossless is important: it works without re-encoding. Video editors that support more complex editing typically re-encode the video, resulting in some loss of resolution.

    Another free program, MP4joiner.org, gave unsatisfactory results.

  4. Install the Video.

    1. Drag and drop the GIF or MP4 file into a slide. In older versions of Powerpoint, GIF files may not animate until you "project" the slide.

    2. Technical: HTML for GIF files:
      <img src="yourfile.gif">


    3. Technical: HTML for MP4 files:
      <video controls>
      <source src="yourfile.mp4">
      </video>
      The word "autoplay" can be inserted after "controls".
Suggestions for clarification or improvements are always welcome.
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