OK, I was wondering about that. So then let's set up a new LOAD option.
Actually, we have the raw capability already, I just turned it off.
Basically there are two load options:
set appendNew TRUE #default
set appendNew FALSE #what you want
I'll set it up so that if you say
set appendNew FALSE
and then
LOAD trajectory....
as long as the files are already a set of trajectories with the same number
of atoms per trajectory, Jmol will simply append a new set of coordinates.
This should be very fast.
Bob
On Fri, Mar 19, 2010 at 8:49 AM, Andrew R Turner <[email protected]>wrote:
>
> Hi Bob,
>
> Yes, that is the situation except that I do not have all the files to
> begin with so I cannot concatenate them.
>
> I am using Jmol to display the results of the simulation as it is
> running. Periodically, the simulation outputs a file representing a
> point on the trajectory. My JavaScript detects that this file has
> appeared and appends it to the model set in the applet.
>
> Unfortunately, as the number of models increases Jmol really slows down.
>
> If, once the simulation is finished, I have the full trajectory in one
> file then I can load and manipulate it with no problems. I would like
> to recreate this behaviour dynamically so that users can watch their
> simulations evolve as they are running.
>
> Cheers
> Andy
>
> Quoting Robert Hanson <[email protected]>:
>
> > I think I understand. You have a set of models, each in a different PDB
> > file, which together represent a set of trajectories -- meaning there is
> a
> > 1:1 homology between atoms in one model to the next.
> >
> > The very simplest way to load these as a trajectory is to concatenate the
> > files into one large file, then read that file as a trajectory. You can
> > still select specific models from that file to load or just load the
> whole
> > thing.
> >
> > Is that perhaps all you need?
> >
> > Bob
> >
> > On Fri, Mar 19, 2010 at 6:59 AM, Andrew R Turner
> > <[email protected]>wrote:
> >
> >>
> >> Hi Angel,
> >>
> >> I probably was not very clear. As I understand it, when you use:
> >>
> >> load TRAJECTORY file
> >>
> >> you get one set of atoms and 'number-of-frames' sets of coordinates
> >> (one set of coordinates for each model/frame in the file).
> >>
> >> All my files will have one model in them. What I want to do is have:
> >>
> >> load file
> >>
> >> to get the initial atom set and initial coordinates. Then have a loop:
> >>
> >> for i=1, nframe
> >> load file(i)
> >> end
> >>
> >> that appends just the coordinates to the data that is already loaded
> >> without creating a new atom set. (This is essentially splitting up the
> >> "load TRAJECTORY file" command into its component parts.)
> >>
> >> set appendNew false
> >>
> >> will not help me I do not think as it will add new frames (which is
> >> what I want to be able to animate the trajectory), it will just append
> >> the atoms in the appended file to the current frame.
> >>
> >> Cheers
> >> Andy
> >>
> >> Quoting Angel Herráez <[email protected]>:
> >>
> >> > Hi Andy
> >> >
> >> > I'm not sure I understand what you mean by adding a trajectory point
> >> > (I haven't worked with
> >> > trajectories), but regarding the addition of atoms without
> >> > generating new frame/model, there
> >> > is
> >> >
> >> > set appendNew false
> >> >
> >> > Don't know if that would fix the slowness.
> >> >
> >> >
> >> >
> >> >
> >>
> ------------------------------------------------------------------------------
> >> > Download Intel® Parallel Studio Eval
> >> > Try the new software tools for yourself. Speed compiling, find bugs
> >> > proactively, and fine-tune applications for parallel performance.
> >> > See why Intel Parallel Studio got high marks during beta.
> >> > http://p.sf.net/sfu/intel-sw-dev
> >> > _______________________________________________
> >> > Jmol-users mailing list
> >> > [email protected]
> >> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >> >
> >> >
> >>
> >>
> >>
> >> ==========================================
> >> Dr Andrew R. Turner
> >> e: [email protected]
> >> t: +44 (0)131 651 3578
> >> p: EPCC, University of Edinburgh EH9 3JZ
> >> ==========================================
> >>
> >> --
> >> The University of Edinburgh is a charitable body, registered in
> >> Scotland, with registration number SC005336.
> >>
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Download Intel® Parallel Studio Eval
> >> Try the new software tools for yourself. Speed compiling, find bugs
> >> proactively, and fine-tune applications for parallel performance.
> >> See why Intel Parallel Studio got high marks during beta.
> >> http://p.sf.net/sfu/intel-sw-dev
> >> _______________________________________________
> >> Jmol-users mailing list
> >> [email protected]
> >> https://lists.sourceforge.net/lists/listinfo/jmol-users
> >>
> >
> >
> >
> > --
> > 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
> >
>
>
>
> ==========================================
> Dr Andrew R. Turner
> e: [email protected]
> t: +44 (0)131 651 3578
> p: EPCC, University of Edinburgh EH9 3JZ
> ==========================================
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
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
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
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http://p.sf.net/sfu/intel-sw-dev
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