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Author Topic: Naming Conventions in x3dna_md output  (Read 3560 times)

Offline gsote

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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).

Thanks,
Gavin

Offline xiangjun

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Re: Naming Conventions in x3dna_md output
« Reply #1 on: June 01, 2012, 11:16:59 pm »
Hi Gavin,

Thanks for using the 'x3dna_ensemble' Ruby script. I am glad you ask "about the naming conventions" of the output parameters. To address your question, it helps to know how the script works -- it calls 'analyze' for each model/snapshot and then extract the corresponding parameters of double helical structures.

Simply run 'analyze' on a single structure, you'd notice the following section at the very beginning of the .out file:
Code: [Select]
1. The list of the parameters given below correspond to the 5' to 3' direction
   of strand I and 3' to 5' direction of strand II.

2. All angular parameters, except for the phase angle of sugar pseudo-
   rotation, are measured in degrees in the range of [-180, +180], and all
   displacements are measured in Angstrom units.
Listing strand II parameters in the 3'->5' direction makes its base numbering consistent with base-pairs in a duplex.

So you are right in assuming "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". However, as noted above, the puckering2 etc parameters are listed in 3'->5' direction.

As a general rule, whenever in doubt with any 3DNA-related issue, check with a concrete example, and do not hesitate to ask on the forum.

Xiang-Jun
« Last Edit: June 01, 2012, 11:19:05 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.