Oddly enough, I had that wrong. What you really wanted was:
load XYZ ....
not
load COORD ...
Hmm.
On Fri, Mar 19, 2010 at 11:29 AM, Robert Hanson <[email protected]> wrote:
> 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
>
--
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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