Matt, good to hear this! Comments below. - Bob
On Wed, Oct 8, 2008 at 10:09 PM, Matthew Zwier <[EMAIL PROTECTED]> wrote:
> Hi all,
>
> A few days ago, Bob Hanson mentioned that improved support for display
> of MD trajectories is on the docket for 11.7. I'm interested in
> surveying the lay of the land and possibly helping out with the coding
> for MD trajectory support. I have a couple questions/thoughts, mostly
> related to what's feasible given the underlying data structures.
>
> 1) Are there plans to support simultaneous display of multiple
> trajectories?
>
The big issue is memory. Jmol can handle about 120,000 atoms (at least on my
machine) before it chokes. Let's make sure we are using the same language.
"Trajectory" is a full sequence, "Trajectory Step" is a single snapshot.
Yes?
So one has to involve some sort of reasonable selectivity here.
The way the file reader works is that any number of models can be loaded
simultaneously. In the case of standard multi-model PDB files, these models
can be read either as totally independent models or as "trajectories" where
only one step can be displayed at a time, because there are only that many
atoms really created. Changing "frames" simply changes the coordinates.
(Like the old CHIIME multiple-xyz file business.)
>
> 1a) If so, I'd be interested in coordinating the animation of
> multiple trajectories according to some global notion of time. This
> would allow for displaying ensembles of trajectories, each of which
> may start and/or end at a different time. I've hacked something like
> this together with multi-frame XYZ files and JavaScript, but it's
> prohibitively slow (each call to "display 1.10,2.5,3.1..." takes
> tenths of seconds on a Core 2 Duo); something internal to the applet
> would be much more efficient.
>
You mean each of these 1, 2, 3 files are each a full trajectory, and you
want to simultaneously overlay x number of trajectory steps? Is that useful?
>
> 2) Are Jmol's data structures amenable to something like the above,
> or would it require enough of a re-write that it would cause more
> trouble than it would solve? I've worked with Jmol before (on the
> development side), but I don't have enough experience to answer that
> one.
>
All depends upon what you really want. Right now you can certainly load
multiple topology files so that, say, 1.1-1.100 are trajectory steps for run
1, and 2.1-2.100 are trajectory steps for run 2. And then you can certainly
display {1.1 or 2.1 or ...}
At least, I think you can.... Supposed to be able to. You are just limited
to one trajectory step from EACH sequence loaded. I can't imagine why that
would take any major amount of time if they are trajectories.
>
> This kind of thing is clearly an edge-case compared to the single
> large trajectory that's so common, but it's something no other
> visualization tool I know of can do (let alone one that can be
> embedded in a web page to monitor a running simulation.) As I said
> above, I'm willing to help out on it if you all think it would be a
> useful thing to have.
>
I'm happy to do the coding if anything is necessary there. Doesn't sound too
involved to me. Keep talking....
>
> Cheers,
> Matt Zwier
>
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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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