Hmmmm... That is an idea. I could just replace the coords as the simulation goes along and then once it has finish load the entire trajectory so you can replay and analyse it.
I will let you know how I get on... 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
