Re: [Jmol-users] large animations

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I've gotten that message and am sorry for that confusion. No, "x" for 
"experimental". Angel reminded me that people use "x" as a generic. So now I'm 
adding a blurb at the top of all my messages relating to "10.x".

[note: this message relates to the experimental prototype "Jmol 10.x" not
the public release Jmol 10.2. See
http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htm for details.]

I messed up and overlaid my new.htm from work with one from home and lost the 
test I was doing for you. Did you get the message that now in 10.x you can move 
atoms around at will, one by one? I'll be very interested to see if that works 
for you. It SHOULD read:

  experimental method to modify atom positions:
  jmolSetAtomCoord() and jmolSetAtomCoordRelative()

  load caffeine.xyz
  # Just <click here> a few times for random changes in atom placement
  # Please let me know if this works
  #

at

http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htm

Bob

eric capps wrote:

> 
> if you have any more advice i'd love to hear it, and when i run into my 
> next wall i'll be right back here.
> 
> btw, if you're curious, this is for a project at 
> http://eon.cm.utexas.edu <http://eon.cm.utexas.edu>

definitely curious. super

> 
> -eric
> 
> On 5/23/06, Bob Hanson <ha...@st... <mailto:ha...@st...>> 
> wrote:
> 
> 
> 
>     Eric Capps wrote:
> 
>      > bob,
>      >
>      > i believe i have the most recent version of jmol, but my jmol.js
>      > doesn't have these functions anywhere in it. the jmol-new.js on the
>      > page you linked me to seems to be older, but it does have these
>      > functions. what's the deal with that? does my version not have that
>      > functionality?
> 
>     oops, sorry, it isn't older -- it's just that I've ignored the header.
>     the two key files are JmolAppletProto.jar and Jmol-new.js in
> 
>     http://www.stolaf.edu/people/hansonr/jmol/test/proto
> 
>     if you use this, comment out your jmolInitialize() call and have
>     JmolAppletProto.jar in the same directory as your HTML page.
> 
>      >
>      > what you are describing sounds very interesting but is
>     unfortunately a
>      > bit over my head, as i'm new to both jmol and javascript. still, i'd
>      > like to give it a shot.
>      >
>      > so am i right in thinking that you are suggesting writing a method
>      > which would perform animation by moving an atom or a group of atoms
>      > rather than reading an entire list of coordinates? this would be
>      > particularly helpful as the animations i am trying to make typically
>      > only have one or two atoms moving at once (out of thousands). would
>      > this be written in the jmol source code or the jmol.js file?
> 
>     Ah, there you go. Then you are all set! Can you figure out which
>     atoms are
>     changing? That's interesting. OK, just for you, Eric:
> 
>     http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htm
>     <http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htm>
> 
>     Fun, eh? This should give you some ideas.
> 
>     It will probably not work on Macs. What are your parameters in that
>     regard?
> 
>     If you want to change a WHOLE LOT of atom positions, though, we
>     should pass the
>     applet a string and let it parse the string for atoms.
> 
> 
>     Bob
> 
> 
>      >
>      > -eric
>      >
>      > On 5/23/06, Bob Hanson <ha...@st...
>     <mailto:ha...@st...>> wrote:
>      >
>      >> what a challenge!
>      >>
>      >> Keeping the orientation after a file load is no problem. Jmol 10.x
>      >> allows the
>      >> following:
>      >>
>      >> jmolSaveOrientation()
>      >> jmolScriptWait("load....")
>      >> jmolRestoreOrientation()
>      >>
>      >> So then the orientation resets to the original. You can see this in
>      >> action at
>      >> http://fusion.stolaf.edu/chemistry/jmol/xtalx
>     <http://fusion.stolaf.edu/chemistry/jmol/xtalx> . There are links in the
>      >> lower
>      >> left panel under "orientation" for "save" and "restore". These work
>      >> across file
>      >> loads.
>      >>
>      >> 10.x also allows proper loading of multiple files. The problem
>     you are
>      >> going to
>      >> run into is that every atom has to be saved individually, so you are
>      >> looking at
>      >> 100000 x (nAtoms) of atoms in memory. Not feasible.
>      >>
>      >> The better solution, it seems to me, would be to have a limited
>     number
>      >> of active
>      >> frames (say, 10) and then actively CHANGE the atom positions as
>      >> needed. Think of
>      >> the set of atoms as a "buffer" that we are going to fill as needed.
>      >> When the
>      >> user is watching frame 3, we are loading frame 2; they go to
>     frame 4,
>      >> we load
>      >> frame 3. Sort of the way a word processor processes a large
>     document.
>      >> It doesn't
>      >> have to load the whole thing -- just what you are looking at. One
>      >> would just
>      >> fill them as needed and display them in some sequence.
>      >>
>      >> So, it seems to me, the solution is to have the capability of
>     loading
>      >> atom
>      >> positions independently of the atoms themselves -- sort of a
>     "replace" or
>      >> "loadCoordinates" capability rather than a "load" capability, and at
>      >> the frame
>      >> level rather than the "model set" level. Or, for that matter, at the
>      >> atom level,
>      >> not the model level.
>      >>
>      >> It would only work for situations where the bonding and atoms were
>      >> identical in
>      >> each "frame", but I think this is what you are thinking. Since
>     all you
>      >> need are
>      >> the xyz coordinates, the syntax is trivial -- I could imagine
>      >> accepting xyz
>      >> files, since they are so simple, but one could also imagine just
>      >> straight x y z
>      >> x y z x y z down the line. A very simple reader.
>      >>
>      >> Maybe the syntax would be something like:
>      >>
>      >> loadCoordinates FILENAME [optional model number]
>      >>
>      >> Personally, I would drive the whole thing with JavaScript based on
>      >> that sequence
>      >> file, and as the frames change and send back their frame-change
>     callback
>      >> message, execute the loads. In fact, if you set up the animation
>     as a
>      >> loop 1 2 3
>      >> 4 5 1 2 3 4 5 1 2 3 4 5, then you get a message back that you are on
>      >> frame X any
>      >> time. The JavaScript would then call to load frame X+3 with file
>     Y+3,
>      >> and the
>      >> animation could just run and run, and the user could twiddle
>     with the
>      >> mouse all
>      >> he/she wants, and it would just be a gas. They could start, stop,
>      >> rewind, etc.
>      >> You would just have to carefully sync the frame loading with the
>      >> user's trajectory.
>      >>
>      >> Certainly doable. Sound interesting?
>      >>
>      >> Bob Hanson
>      >>
>      >>
>      >>
>      >> Eric Capps wrote:
>      >> > i'm trying to create a very large animation. it maps the
>     movement of
>      >> > around 1000 atoms, over potentially hundreds of thousands of
>     steps,
>      >> > with as many as 10000 unique states (there are situations where a
>      >> > series of steps repeat themselves many times). i am new to
>     jmol, and
>      >> > from the demonstrations it seems that animation only works on
>      >> > multi-frame files. for hundreds of thousands of steps, this is
>      >> > unfeasible.
>      >> >
>      >> > i have each unique state stored in its own .xyz file, and
>     another file
>      >> > which lists the order in which they occur. i thought to make a
>      >> > multi-frame .xyz of only the unique states and specify them by
>     frame
>      >> > number when they repeat, but this still creates a very large file
>      >> > (around 100 megs), far larger than i feel it has to be.
>      >> >
>      >> > now, i am trying to create a script which uses load statements as
>      >> > necessary to load the next, potentially repeated .xyz file,
>     but i want
>      >> > the user to be able to make changes to the view and have them
>     not be
>      >> > reset every time a new .xyz is loaded. is this possible? if
>     not, does
>      >> > anyone have any ideas on how to implement very large animations?
>      >> >
>      >> > thanks,
>      >> > eric
>      >> >
>      >> >
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>      >>
>      >> --
>      >> --
>      >>
>      >> Robert M. Hanson, ha...@st...
>     <mailto:ha...@st...>, 507-646-3107
>      >> Professor of Chemistry, St. Olaf College
>      >> 1520 St. Olaf Ave., Northfield, MN 55057
>      >> mailto:ha...@st... <mailto:ha...@st...>
>      >> http://www.stolaf.edu/people/hansonr
>     <http://www.stolaf.edu/people/hansonr>
>      >>
>      >> "Imagination is more important than knowledge." - Albert Einstein
>      >>
>      >>
>      >>
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>      >
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>     --
>     --
> 
>     Robert M. Hanson, ha...@st... <mailto:ha...@st...>,
>     507-646-3107
>     Professor of Chemistry, St. Olaf College
>     1520 St. Olaf Ave., Northfield, MN 55057
>     mailto: ha...@st... <mailto:ha...@st...>
>     http://www.stolaf.edu/people/hansonr
> 
>     "Imagination is more important than knowledge." - Albert Einstein
> 
> 
> 
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-- 
--

Robert M. Hanson, ha...@st..., 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:ha...@st...
http://www.stolaf.edu/people/hansonr

"Imagination is more important than knowledge." - Albert Einstein

Re: [Jmol-users] large animations

An interactive viewer for three-dimensional chemical structures.

Re: [Jmol-users] large animations