Hi Bob, Excellent! This works really well. Thanks for all your help.
Just to put it in context... This is all for the Royal Society Summer Science exhibition in London in the Summer (http://www.summerscience.org.uk). I am helping a group from University College London set up an exhibit to allow anyone to run simulations on the UK national supercomputing facility, HECToR (http://www.hector.ac.uk), from a web interface and watch the simulation progress as the computer spits out the results. I will let you know once we have this exhibit up and running so you can see it in action. Cheers Andy Quoting Robert Hanson <[email protected]>: > 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 >>>> >> > 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 >>>> >>> >>> >>> >>> -- >>> 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 > ========================================== 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
