Hi Jeff, Good idea and I have just tried this. Unfortunately, I see a lot of slowdown as the simulation progresses again. This time it is due to the size of the model being loaded increasing as I add more and more points.
Maybe I will see the slowdown whichever method I use. I just thought it may be that if I was able to load a trajectory piecemeal then I would be able to get the best of both worlds, that is: * Loading the entire trajectory from one file - long load time but manipulation works well once loaded. * Loading each trajectory point as a new model - short load times but Jmol struggles to handle the size of the dataset. Cheers Andy Quoting Jeff Hansen <[email protected]>: > 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. >> > >> > >> > >> > >> ------------------------------------------------------------------------------ >> > 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 >> ------------------------------------------------------------------------------ >> 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
