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
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