Nick,
Ah, frames and models. It's more interesting than that. Here is the
correlation:
PyMOL object --> Jmol selectable/displayable atom set, isosurface, CGO
(also new to Jmol), or measurement
PyMOL state --> Jmol MODEL
PyMOL frame --> new Jmol FRAME option
PyMOL movie --> new Jmol ANIMATION option
PyMOL scene --> Jmol scene (new to Jmol)
PyMOL has a complex relationship between "frames" and "states" -- both
appear to be the same in some cases, but in movies there is a distinction.
Multi-model PDB files are pulled in as separate states. Appended files,
though, are all pulled into the same state. And so it gets a bit
complicated.
Movie frames point to states. For example, in a PyMOL "morph", the movie
"frames" are just pointers to different states; in scripted movies, though,
frames run scripts that may pull in a new scene, which can specify a state,
or just change some aspect of the rendering. The second type of movie is
not reversible; the first is much like standard animation in Jmol, although
there's an N:1 mapping of frames to states, unlike the standard 1:1 mapping
for Jmol. A new Jmol animation option lets you run an arbitrary sequence of
states, recreating the morph-type PyMOL movie:
anim FRAMES [1 1 1 1 1 2 3 3 3 3 4 5...]
Scenes are completely different. Sort of like Jmol states, but not as
reproducible, because they don't store global settings. I've been able to
implement PyMOL scenes in Jmol as a completely new idea to Jmol -- kind of
like states, but without the file loading. They show up on a new pop-up
menu item "Scenes" just above "Zoom" -- so far, that is working. Sure to be
some surprises.
Lots of little additions to Jmol to accommodate PyMOL features; no
documentation yet, of course, other than
http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Bob
On Fri, May 31, 2013 at 7:30 AM, Greeves, Nick <ngree...@liverpool.ac.uk>wrote:
> Hi Bob,
> I must have stumbled into this functionality without realising it wasn't
> official yet!
>
> I had created http://138.253.125.70/~ng/Demo/jsmol/galleryIPython.htmland
> noted that JSMol seems to "flatten" PyMOL frames into a single model.
> In this example (not mine) I think the substrates are in different frames.
>
> Otherwise it looks great!
>
>
> All the best
> Nick
> --
> 3D Organic Animations http://www.chemtube3d.com
> Tel: +44 (0)151-794-3506 (3500 secretary)
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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