Annemarie Honegger wrote:
>However, since most other commands in the
>"Jmol interactive scripting" documentation work equally well entered
>in the console or
>collected in a script that is then loaded with the "script" command,
>a warning in the documentation might be appropriate.
>
>
>
right, if that is happening, then it is a bug. Say again exactly what
can't be done. When I test, I can have load "" in a script as well as
from the console.
>Coming to think of it - it would be very nice if one could save the
>current transformation over such a reload,
>e.g by saving the current transformation matrix before the reload
>and re-applying it afterwards
>
>
Ah, this is a project I started WAY back in March or April -- the idea
is to not just save the orientation (easy) but the actual "state" of the
molecule. I made some progress on that front, but it has required
substantial recoding throughout Jmol to make it more "state" aware. To
date we don't have such a mechanism. The JavaScript to do this is:
jmolSaveOrientation("savename")
jmolSciptWait(.....)
jmolRestoreOrientationDelayed(0.0, "savename")
(I see there is a mistake in Jmol-11.js as I write this. The following
should work:
jmolSaveOrientation("savename")
jmolSciptWait(.....)
jmolRestoreOrientation( "savename")
but it throws in a 1-second delay. Next iteration of Jmol-11.js will fix
this.)
But I agree that a little save/restore in Jmol might be a nice idea as
well. Very simple for orientation.
How about
save orientation "orientationID"
load ""
restore orientation "orientationID" nSeconds
Then in the future there might be some other types of "save" and
"restore" options -- zoom, center, rendering, visibility, etc.
Side-chain hydrogen bonds:
---------------------------
I'm not presently working on this. One of the major issues there is
sprouting the hydrogens and getting the hybridization right for both
proteins and nonproteins. Also an issue is the rotational freedom around
the C-O-H bond of alcohols and phenols. Is there a general solution to this?
Bob
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