From: Tim M. <ti...@mm...> - 2005-07-19 17:39:28
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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 switch somewhere because i can't imagine the hardware is already at it's limit. 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. 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... Tim |