I don't think that is what he needs. How about this idea though. Rather than
append points to the trajectory as you go along. Concatenate those points to
the end of your trajectory file then reload the trajectory. So, when you read
in the initial file and initial trajectory I assume that trajectory file has
just one point. As you generate new points along the trajectory you need to
add those points to the end of the trajectory file. The trajectory file is
just a text file right? So write the new coordinates to the end of that text
file then reload the trajectory file. This I believe would all be done outside
of Jmol using javascript (to rewrite the trajectory file) then tell Jmol to
reload the trajectory file. Is that what you need?
***********************************************
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[email protected]
***********************************************
On Mar 19, 2010, at 8:34 AM, Robert Hanson wrote:
> 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.
> >
> >
> >
> > ------------------------------------------------------------------------------
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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.
>
>
>
> ------------------------------------------------------------------------------
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>
> --
> 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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------------------------------------------------------------------------------
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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