I've got a structure at time point 0. This is the reference. I want to see, how it changes through time, so I want it to be rendered throughout the animation.
I have a simulation, and from that I create a pdb file, that contains many models, each representing a timepoint. And when I say many models, I mean e.g. 1000, or more.
So even when the system is very small (only 30 aa) the pdb file has a considerable size. (~20% compressed...) so I don't really want to double it up, if not necessary.
under "swim away" I mean that during md, the protein rotates, and shifts, but that's not really important.
basically I want to fake multi chain pdb files by loading separate ones in the same time...
On 2/2/06, Miguel <
[EMAIL PROTECTED]> wrote:
> If I would like to do something like that, where should I start looking in
> the source code?
Supporting the general case of loading more than one molecular model file
is a *huge* job that would impact the entire system.
If it were straightforward then it would already have been done.
> what I want to do is the following:
> I have a structure, which I run through a molecular dynamics simulation.
> I want to render the initial structure as a reference, and watch how the
> structure changes in course of the simulation.
> For that, I have a multi-model pdb file, which plays nicely in jmol. I
> superimposed every frame with the reference, so the molecule won't "swim
> away" through time.
Good.
So, that is one file with multiple models.
> If I understand things correctly, I could create a pdb file, where each
> model has 2 chains with the reference and the simulated structure, but
> that
> would double up the already considerable sized pdb file (and wastes cpu
> time, memory, etc.).
I don't understand what you mean by the 'reference' ... and am not exactly
sure what you mean by 'swim away' through time.
Nevertheless, I suspect that is the correct solution.
Don't worry about the memory and space. I suspect that anything that is
small enough to run through a molecular dynamics simulation is too small
to worry about.
Miguel
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