What this tarball contains
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This tarball contains the .pm3 files and scripts used to generate the kymographs in the paper "Direct simulation of the self-assembly of a small DNA origami."

How to parse the .pm3 files
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The files were used to generate the kymographs in the paper "Direct simulation of the self-assembly of a small DNA origami," and describe the state of the simulated system at different points in time during the simulation. 

Each snapshot (point in time) is labelled by the number in the first column. There is a blank line separating the data from each snapshot. Within each snapshot, there are 49 lines, which correspond to the 48 lines of data in the kymograph (the amount of misbonding in each of the 24 scaffold domains, plus the amount of native bonding/blocking in each of the 24 domains), plus a dummy line (labelled 48) which (most likely) is necessary to make the script that makes the kymographs work. The second column indexes these lines. The third column gives the state of the relevant aspect of the domain it refers to. 

For the following description we'll think about a line where the first column's value is X, the second column's value is Y, and the third column's value is Z. 

MISBONDING:
For Y=0, Z gives the amount of misbonding in domain 1; for Y=2, Z gives the amount of misbonding in domain 2; and so on. For misbonding, the number of misbonded base pairs in that domain corresponds to the number Z. It must be in the range 0-16 inclusive.

NATIVE BASE PAIRING AND BLOCKING:
For Y=1, Z gives the amount of native base pairing or blocking in domain 1; for Y=3, Z gives the amount of native base pairing or blocking in domain 2; and so on. A value of Z in the range 32-48 inclusive indicates native base pairing. The number of native base pairs is given by Z-32. A value of Z in the range 64-80 inclusive indicates blocking. The number of blocking base pairs is given by Z-64.

Example
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The line

10257955625 5 79.000000

means that, in simulation time step 10257955625, domain 3 of the scaffold strand was experiencing staple strand blocking with 15 blocking base pairs in the domain.


Ben Snodin 21/08/15
