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
