how excellent! Good job, Rich. Thank you for sharing this.
Just a couple of comments:
The default for Jmol is to render a structure with 100% zoom scaled to
the larger of width and height. When using different dimensions (800
width and 600 height in this case), I recommend you:
1) Use set zoomLarge false to ensure that the model at 100% is
fully visible. Not entirely necessary, but I always do this, myself.
2) As you note there, you can generate JPG files at any dimension
regardless of the current Jmol window. Still, I suggest you make your
Jmol window also 800 x 600 so that you have no surprises in the images
created. With the application this can be done by starting Jmol with
jmol -g 800x600
Also, with that in mind, note that the -j flag on the application now
allows scripting on the command line. So you could get all that on a
command line and create the movies entirely in batch mode. Other
command line flags such as -ion could be of use here. From jmol -h:
-o,--noconsole no console -- all output to sysout
-g,--geometry window width x height, e.g. -g500x500
-x,--exit exit after script (implicit with -n)
-i,--silent silent startup operation
-j,--jmolscript Jmol script to execute
-n,--nodisplay no display (and also exit when done)
To combine command-line scripts with file-based scripts, use the -j
flag and include in it ".....;script file1.txt;script file2.txt"
Quotes may be tricky -- use \" with the -j "...." for Jmol commands
that need quotation marks.
Bob
Bob
On Wed, Dec 3, 2008 at 8:26 AM, <[EMAIL PROTECTED]> wrote:
> With Bob's implementation of quaternions in Jmol it is *extremely* easy to
> let Jmol create an image sequence between two user-defined views. This
> sequence can then be converted into a movie using the standard tools. I
> did this recently (with Bob's help to get the syntax right) using the
> application and was pleasantly surprised at how well it worked.
>
> The steps are simple. In a text editor make two scripts, the first
> ("settings.txt") will be the settings you want, e.g. axes off, unitcell
> off, spacefill..., etc.
> and the second will have the commands to create the image sequence
> ("make_movie.txt") which I go into detail about below:
>
> In the Jmol application:
>
> 1) load a molecule and open the script window and enter
> script settings.txt
> to setup Jmol and your molecule to taste
>
> 2) move the molecule to the first view and in the script window enter
> q1 = script("show rotation")
>
> 3) move the molecule to the final view and in the script window enter
> q2 = script("show rotation")
>
> 4) now reset Jmol and return to the first view with these commands
> reset; script settings.txt; rotate quaternion @q1
>
> 5) now start the make_movie script with
> script make_movie.txt
> and Jmol will start writing the images
>
> In the make_movie.txt script are these commands:
>
> # define the number of images to create in the variable num_frames
> # for a 15 fps video lasting 30 sec we need 450 images
>
> var num_frames = 450
>
> # assuming the two quaternions defining the views are q1 and q1 then
> # the fraction the model must be moved for each frame to get from
> # view q1 to view q2 is q2/q1/num_frames, define this as dq
>
> var dq = q2/q1/num_frames
>
> # now use a loop to create the images writing to a filename created
> # on the fly with a sequence id (using PNG files in this example)
>
> for (var i = 0; i <= num_frames; i = i+1)
> var filename = "movie"+("000"+i)[-2][0]+".png"
> write IMAGE 800 600 PNG @filename
> rotate quaternion @dq
> end for
>
>
> --Rich
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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