Tim, I replied to you4 posting a few days ago:
---------------------------- Mensaje original ---------------------------- Asunto: Re: Atom number limits in Jmol 10 De: "Miguel" <[EMAIL PROTECTED]> Fecha: Jue, 14 de Julio de 2005, 21:50 Para: [EMAIL PROTECTED] -------------------------------------------------------------------------- Tim wrote: > hi jmol developers, hola miguel > > our lab is using the jmol applet to visualize pbd from our webserver. we'd also like to use it to show trajectories but we ran into 2 problems: > > first: using the nmr-pdb (MODEL 1 ... ENDMDL MODEL 2 ... ENDMDL etc) we get an JavaOutOfMemory problem when we try to charge e.g. 100 frames of 2000 atoms each. I didn't get too far into the code but is there a MaxAtoms or MaxFrames There are no limits on number of atoms or number of frames. > switch somewhere because i can't imagine the > hardware is already at it's limit. The Java virtual machine is running out of heap memory space. By default, the Java virtual machine will only allocate 128Mb of ram for heap space. I recently changed the shell & bat files for the Jmol application so that they allocate 512M using a command line argument java -Xmx512M -jar JmolApplet.jar I regularly load and check the full rhinovirus with 397K atoms. It is only one frame, not a series of frames like you have. But there should be no difference. > second: our traj become unpleasantly heavy (>10MB) and the user sits in front of a black screen until the very last frame is loaded so i would like to get an estimation of how dificult it would be to get jmol to begin the visualisation of the first frames while still loading later ones. and where in the code one would have to start looking to make relevant changed. This is impossible with the current Jmol architecture ... sorry. > third: we have developed a file format using eigenvectors and their projections which would allow to construct the entire trajectory quickly and at low resolution from just a few eigenvecs and then iteratively increase resolution by incorporating more eigenvecs while the protein is already on the screen. we're about to write a reader for that format but again it would be nice to get the visualisation while the coords are beeing refined. > > thanks for all comments, i understand that the purpose of jmol was not to show trajectories but if it's tecnically doable why not... Q: What is a 'trajectory'? Miguel ----- Open Source Molecular Visualization www.jmol.org [EMAIL PROTECTED] ----- ------------------------------------------------------- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
