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
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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
>
--
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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