Really, that simple? Well, that sounds like a very efficient solution. Let's
leave it at that then for now, shall we?
On Fri, Mar 19, 2010 at 11:17 AM, Andrew R Turner <[email protected]>wrote:
>
> Hi Bob,
>
> Excellent! This works really well. Thanks for all your help.
>
> Just to put it in context... This is all for the Royal Society Summer
> Science exhibition in London in the Summer
> (http://www.summerscience.org.uk). I am helping a group from
> University College London set up an exhibit to allow anyone to run
> simulations on the UK national supercomputing facility, HECToR
> (http://www.hector.ac.uk), from a web interface and watch the
> simulation progress as the computer spits out the results.
>
> I will let you know once we have this exhibit up and running so you
> can see it in action.
>
> Cheers
> Andy
>
> Quoting Robert Hanson <[email protected]>:
>
> > Andrew, how many trajectory models are we talking about here? If you
> don't
> > need a RECORD of the trajectory, or you feel you can re-use points, you
> > could also use
> >
> > load COORD
> >
> > which just replaces the coordinates -- no slow down, no extra memory at
> all.
> >
> >
> > Just a thought. But I'll get that other set up.
> >
> > Bob
> >
> > On Fri, Mar 19, 2010 at 10:40 AM, Robert Hanson <[email protected]>
> wrote:
> >
> >> I mean
> >>
> >> Load APPEND trajectory...
> >>
> >>
> >> On Fri, Mar 19, 2010 at 10:39 AM, Robert Hanson <[email protected]
> >wrote:
> >>
> >>> 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
> >>>
> >>
> >>
> >>
> >> --
> >> 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
> >>
> >
> >
> >
> > --
> > 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.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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