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Questions and answers => General discussions (Q&As) => Topic started by: Asmita on September 02, 2013, 04:11:43 am

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Title: stacking area overlap
Post by: Asmita on September 02, 2013, 04:11:43 am

Dear users,

I found that x3dna gives the stacking area overlap between base-pairs/steps. But that only includes are overlap between paired bases. If i want to calculate stacking area between single stranded base residues say consecutive bases in an RNA loop..can it be done in 3DNA?

Thank you

Asmita

Title: Re: stacking area overlap
Post by: xiangjun on September 02, 2013, 10:34:37 am

Hi Asmita,

For overlap areas along consecutive bases, the following command should do the trick:

Code: [Select]

find_pair -s INPUT.pdb stdout | analyze stdin
# check output file 'INPUT.outs'
Here assuming your PDB input file is INPUT.pdb. Note the -s option, which treats each nt along a strand consecutively. The output file has extension .outs instead of the normal .out for a duplex.

Note also that DSSR (http://forum.x3dna.org/rna-structures/dssr-software-for-defining-the-(secondary)-structures-of-rna/) has a --non-pair option which characterizes non-pairing interactions, i.e. base-stacking and H-bonding.

HTH,

Xiang-Jun

Title: Re: stacking area overlap
Post by: Asmita on September 02, 2013, 11:44:00 am

thanks dr Lu for the help..

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.