stacking area overlap

[Asmita]

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

[xiangjun]

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 has a --non-pair option which characterizes non-pairing interactions, i.e. base-stacking and H-bonding.

HTH,

Xiang-Jun

[Asmita]

thanks dr Lu for the help..