cdxmorph — animate one ChemDraw structure into another
======================================================

WHAT IT DOES
  You give it ChemDraw drawings; it makes a smooth animation of one
  structure turning into the next. It does not do any chemistry — it
  treats your drawing as artwork and moves the lines and letters.


STARTING IT
  Unzip this folder somewhere you can find it again (Desktop is fine),
  then:

    Mac      double-click   Start cdxmorph (Mac).command
    Windows  double-click   Start cdxmorph (Windows).bat

  A black or white text window opens. Ignore it — it is just the engine
  running. Your web browser will open by itself after a moment.

  Leave the text window open the whole time you are using cdxmorph.
  Closing it stops the program. That is also how you quit.

  THE FIRST TIME you do this it will say it is setting up, and take a
  few minutes; it is downloading the pieces it needs, so you must be
  online. Expect it to use roughly 150-250 MB of disk space, all of it
  inside this folder. Every time after that it starts in a few seconds
  and needs no internet at all.

  To remove cdxmorph completely, drag this whole folder to the Trash.
  It puts nothing anywhere else on your computer.


IF YOUR MAC SAYS IT CANNOT BE OPENED
  macOS blocks files that arrived by email until you allow them once:
  right-click (or Control-click) the .command file, choose Open, then
  click Open in the box that appears. You only do this once.

IF YOUR MAC ASKS YOU TO INSTALL DEVELOPER TOOLS
  Click Install and wait for it to finish, then double-click the
  .command file again.

IF IT SAYS IT CANNOT OPEN A CONNECTION
  Security software on some managed computers blocks programs from
  opening a local connection. The message will suggest trying a
  specific port; if that also fails, your IT contact will need to
  allow it.

IF NOTHING HAPPENS ON WINDOWS
  Windows may warn that it protected your PC. Click "More info", then
  "Run anyway". If it says Python is missing, it will open the download
  page for you — when you install Python, tick the box that says
  "Add Python to PATH", or it will not be found.


USING IT
  1. Choose your file. Either ONE ChemDraw file containing the whole
     scheme (structures separated by arrows), or TWO files — a starting
     structure and a product.

  2. It shows you each arrow in your scheme and how well it matched the
     atoms up by itself. "Bonds carried" is the number to watch: the
     higher it is, the more of the drawing genuinely moves instead of
     fading out and back in.

  3. Where that number looks low, click "edit pairing" for that step.
     You will see both structures with numbered atoms. Click an atom on
     the left, then the atom on the right it should become. Bonds that
     would break turn red and bonds that would form turn green, and the
     tally updates as you go — aim to get the red count down. Click
     "Save pairing" when you are happy.

  4. Press Render. The animation appears on the page. Adjust the speed,
     size or format and press it again as often as you like.

  5. Download it with the link under the animation.


WHAT TO TELL ME
  Anything that looks wrong in the animation is worth reporting, even
  if you cannot say why. Especially useful:

    - a bond or letter that jumps, blinks, or changes length suddenly
    - a bond that should slide across but fades out and back in instead
    - anything that reads as broken, detached, or in front when it
      should be behind
    - structures that turn inside-out or squash flat on the way through
    - anything confusing about the page itself

  If you can, say WHICH step of the scheme and roughly WHEN in the
  animation, and send the ChemDraw file you used.


NOTES
  Your files never leave your computer. Everything runs on your own
  machine; the browser is only being used as the screen.

  Big or long animations take a while — roughly a second of waiting per
  hundred frames. If you want a quick look, lower the seconds-per-step
  or the frames-per-second first, then turn them up for a final version.

  The animation resets if you close the text window, but your ChemDraw
  files are untouched — you can start again any time.
