Re: [Jmol-users] multi-frame .xyz files & pdb MODELs

[timothy d. <mol...@ma...>]

at 5.36p EDT on 2004 February 25 Wednesday Oliver St=C3=BCker said:

> Hi Miguel,
>=20
> Miguel Howard wrote:
> > Q: How do the scripting commands affect animations?
>=20
> I'm not sure what you mean. Do you have something special in mind?
>=20
> After you have started the animation, you can send other script=20
> commands, which are performed without stopping the animation.
>=20
> > Q: When you apply commands like 'wireframe 0.1' does it affect all the
> > atoms in all frames?
>=20
> Yes.
>=20
but you do have fairly fine control over this effect in a pseudo-NMR file;
e.g.,

   select model=3D1
   wireframe 0.1



> > Q: Is there a way to selectively address individual frames (or perhaps
> > better said, the atoms of individual frames) of an animation?
>=20
> No.
>
again, maybe not for the XYZ format, but you can in a pseduo-NMR file.  sin=
ce
each 'frame' is essentially a separate structure, use the model syntax as
above:

   select model=3D3 and nitrogen
   color blue



so this might be the basic start of a pseudo-NMR 'animation':

   restrict model=3D1
   color red
   wireframe 0.3
   delay 0.5
   restrict model=3D2
   color green
   wireframe 0.3
   delay 0.5
   restrict model=3D3
   color blue
   wireframe 0.3
   delay 0.1
   loop
  =20

I use the term 'animation' loosely here; it is nothing like the move comman=
d,
which interpolates positions between start and end and performs a smooth
transition.  this is more like the old style cel-based cartoons ;-)


  =20
> (At least I haven't found a way to do so. ;-) On the other hand even the=
=20
> "select"-command is missing in the current Chime-documentation. :-( )
>=20
> >>and the following commands are available as Chime embed tags:
> >>
> >>animfps=3D###
> >>animmode=3D{loop|once|palindrome|ping|pong}
> >>startanim=3D{false|no|true|yes}
> >>AnimFrameCallback=3D{JSFunctionName}
> >=20

AFAIK, anim params do not apply to pseudo-NMR files.  instead, you can use
'loop' to set up a repeating loop of an animation.  and you can use 'delay'
to (somewhat roughly) control the frame rate.  but it is kludgy, I admit.
I've managed to produce several hundred 'animations' using psuedo-NMR files
and it takes a great deal of customization to make it work well.

AFAIK (again), xyz files are generally useful for small molecules but not f=
or
larger macromolecules.  but maybe that's not quite accurate?


regards,

:tim

--=20
timothy driscoll
molvisions - molecular graphics & visualization
<http://www.molvisions.com/>
usa:north carolina:wake forest