On Thu, Apr 21, 2016 at 9:37 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Thanks Hai,
>
> Is it yours? It's odd no one claims credit on it.
No it's not mine. It was written by Alexander Rose: https://github.com/arose
> The embedded demo
> fails to display the molecule by the way.
>
>
I guess NGL requires more modern web browser. It works fine with my Chrome
browser (Version 49.0.2623.112 m):
https://github.com/hainm/amber_things/blob/master/things/ngl/website/ngl.png
Not sure if this is related to your interest, but in AMBER16 (soon), both
sander and cpptraj have Python API,
which makes them more flexible to plug to other language like Python or
Javascript.
Hai
> Bill
>
> On 4/21/16 6:17 PM, Hai Nguyen wrote:
> > Hi Bill
> >
> >> Or heard of javascript for rendering a live trajectory on a web page?
> > I don't know if there is one like this. But for rendering trajectory on
> > web, you can check NGL viewer: *http://arose.github.io/ngl/
> > <http://arose.github.io/ngl/>*
> >
> > (Choose *Examples --> gro_trajectory*). It has nice API and you can
> easily
> > adapt its code.
> >
> > Hai
> >
> > On Thu, Apr 21, 2016 at 8:25 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> For interactivity, I'd have sander read forces and write measurements
> >> from/to sockets at each step, and I'd perhaps want to build in
> >> geometrical analysis to quickly get, say, the instantaneous angle
> >> between two DNA bases, although pipelining a few hundred atoms through
> >> cpptraj might not take too many milliseconds. Then I'd need to figure
> >> how to map the user clicks and drags happening on the totally different
> >> photos on my web page to reasonable forces in the simulation. I'd want
> >> to display the dynamics occurring as well, perhaps charging high prices
> >> to see behind the scenes :-.) A feedback time of 1 sec (running a few
> >> steps after the mouse click's impact) might suffice.
> >>
> >> Has anyone tried adding structure analysis to sander? Or heard of
> >> javascript for rendering a live trajectory on a web page?
> >>
> >> Bill
> >>
> >> On 4/19/16 12:19 PM, Bill Ross wrote:
> >>> I have been working on an artificial intelligence that aims to
> >>> communicate with pictures:
> >>>
> >>> http://phobrain.com
> >>>
> >>> The idea is to simulate presence on the level of what you feel looking
> >>> into a dog's eyes, a modified Turing Test if you will.
> >>>
> >>> Like in the Wizard of Oz, I have been looking for parts for my
> >>> character, and I'm thinking an md simulation might serve as a heart.
> For
> >>> this, I would need to pull data from the live simulation, and ideally
> >>> introduce forces derived from the clicks of users on the web page. Has
> >>> anyone done this with AMBER or another md program?
> >>>
> >>> Thanks,
> >>> Bill
> >>>
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Received on Thu Apr 21 2016 - 20:00:04 PDT
