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
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>> >> >
>> >>
>> >>
>> >>
>> >> ==========================================
>> >> 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
------------------------------------------------------------------------------
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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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