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Author Topic: using 3DNA for irregular nuc. structure  (Read 4437 times)

Offline bala

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using 3DNA for irregular nuc. structure
« on: April 16, 2007, 09:22:52 am »

I have a RNA duplex with a bulge on one strand.   I want to calculate the helicoidal parameters by excluding the bulge part.  When i run the find_pair followed by analyze, it takes the whole structure and analyze.  To be precise, is there any way that i can do the analysis only on a specific portion of my interest.  

It would be highly helpful if someone could wite me your experience (some ref's) on using 3DNA for irregular nuc. acid structure.


Offline xiangjun

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« Reply #1 on: April 16, 2007, 09:50:13 pm »
"find_pair" generates an input file in text format that you can edit to suit your specific need before feeding into "analyze" (or "cehs").

Just imagine the situation without access to "find_pair": how would you prepare (from a nucleic acid containing structure in PDB format) an input file for an analysis program such as Curves etc?

In the 3DNA homepage, I have also maintained a list of citations to 3DNA compiled from Web of Science. It is not  necessarily complete, but could serve as a good starting point to related published work.

So far, I've been the only person in answering questions in the forum. That's fine as a starting point. In the long run, I do hope other colleagues would get more actively involved: not only in asking questions, but also in answering them; moreover, in sharing your experiences, or contributing scripts/programs etc. Your contribution can make a difference!


Dr. Xiang-Jun Lu [律祥俊]


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.