3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: jyvdf3asdg2 on May 11, 2012, 12:34:39 pm

Title: Extracting base-pair structural context from 3DNA output files of RNA
Post by: jyvdf3asdg2 on May 11, 2012, 12:34:39 pm: First off, thanks for developing such an amazing tool.

To my question, I was reading the paper related to the BPS Database (doi: 10.1093/nar/gkn676) and in it they seem to imply they derive the structural context of base pairs (ie. Helical-Helical, Terminal helix-Helical stretch, etc) from some 3DNA output.

I've looked through the output files of a few simple RNA's I've run with your software but do not see this information anywhere. Am I missing something? Is this information not given by 3DNA directly? Or was it somehow indirectly derived by other output parameters by the authors of the BPS database?

Thanks!
Title: Re: Extracting base-pair structural context from 3DNA output files of RNA
Post by: mauricio esguerra on May 11, 2012, 12:52:31 pm: Hi,

As far as I understand such information is obtained by parsing PDB files and 3DNA output using an (afaik) unpublished python parser called X3DNA-Parser by Yurong Xin.

You can find her e-mail address at:

http://epigenomics.columbia.edu/wordpress/?page_id=6

Perhaps you can drop her a line. I remember vaguely that perhaps she had a UML diagram of the parser in her PhD thesis.

Cheers,

M.
Title: Re: Extracting base-pair structural context from 3DNA output files of RNA
Post by: jyvdf3asdg2 on May 11, 2012, 01:06:45 pm: Hi esguerra,

Thanks so much. That's it.

Quote from: esguerra on May 11, 2012, 12:52:31 pm
Hi,

As far as I understand such information is obtained by parsing PDB files and 3DNA output using an (afaik) unpublished python parser called X3DNA-Parser by Yurong Xin.

You can find her e-mail address at:

http://epigenomics.columbia.edu/wordpress/?page_id=6

Perhaps you can drop her a line. I remember vaguely that perhaps she had a UML diagram of the parser in her PhD thesis.

Cheers,

M.