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MD simulations / Naming Conventions in x3dna_md output
« on: June 01, 2012, 01:35:37 pm »
Hi All,
   I have a quick question about the naming conventions in the ruby scripts.  First of all, they work fantastically, and I'm pretty sure I can identify the output correctly but since I can't find documentation specifically stating it I don't want to make any assumptions before I use the data I've generated.  My question is simply about the naming conventions used.
  When I extract a time series of a parameter, say puckering, I can use puckering1 or puckering2.  I assume that puckering1 refers to the pucker data from strand1 and puckering2 refers to data from strand2.  I also assume that column 1 generated by extracting puckering1 refers to base 1 in the 5'->3' direction, but I'm not sure about puckering2 and strand 2.  I assume it also lists 5'->3' meaning that column 1 is base 1 in strand 2 going from 5'->3' (as labeled in the files generated by find_pair).


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