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Messages - sharanr2

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RNA structures (DSSR) / Re: Phosphodiester bond length
« on: June 10, 2016, 10:13:09 am »
Thank you for your response.

Is there any parameter that would measure the length of that gaps in the backbone? In the output file, DSSR recognizes there is a break in the chain in the summary of structural features section.

In the actual structure, those two bases are bonded by phosphodiester linkages, making a kissing loop between the A and B chains.

RNA structures (DSSR) / Re: Phosphodiester bond length
« on: June 09, 2016, 01:48:44 pm »
Thank you for your quick response.

I am hoping to use DSSR to characterize "good" structures from "bad" ones for use in a scoring function for structure prediction. For example (structure attached), if there is a large gap in a backbone, I would like to be able to quantify how large that gap is (these gaps longer than actually possible). The two nucleotides are in sequential order (base 5 and base 6) in the same strand (A). The distance is around 8 Å. I have tried adding an explicit connect statement between the P and the O3' of two nucleotides but that did not seem to change anything.

RNA structures (DSSR) / Phosphodiester bond length
« on: June 09, 2016, 10:16:33 am »

I was wondering if there was a way to see phosphodiester bond lengths in the backbone of an RNA structure? The closest I have found is the Dp field in the dssr-torsion.txt file, however, if the distance appears to be too long, it is not calculated, but a "---" is there.

Please let me know if this is possible or if you need more information/examples. Thank you.

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The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.