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Hi Xiang-Jun,
I came across this particular capping interaction where
the O4' that is supposed to be stacked over a G is slightly off
the five membered ring. Is that expected since I thought
that such interactions were strictly above the base.
Please see attached figure.
This is the dssr output line:
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List of 5 atom-base capping interactions
dv: vertical distance of the atom above the nucleotide base
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type atom nt dv
1 sugar O4'@..M.G.167. ..M.G.166. 3.36
Best,
Pascal
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Hi Pascal,
The slightly off capping of O4' over the five-member ring is as expected since internally DSSR adds an small offset to allow for boundary cases.
Xiang-Jun
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Thanks for the reply Xiang-Jun.
Can this be parametrized ? That would be nice
since I would prefer no offset.
Also, how much is that offset ?
Best,
Pascal
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You can remove the offset by specifying the option --polygon-offset=0. The default is 0.27 A.
HTH,
Xiang-Jun
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.