3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: auffinger on February 14, 2015, 11:16:22 am

Title: possible issue with capping interaction
Post by: auffinger on February 14, 2015, 11:16:22 am: 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:

****************************************************************************
List of 5 atom-base capping interactions
dv: vertical distance of the atom above the nucleotide base
-----------------------------------------------------------
type atom nt dv
1 sugar O4'@..M.G.167. ..M.G.166. 3.36

Best,

Pascal
Title: Re: possible issue with capping interaction
Post by: xiangjun on February 14, 2015, 12:49:33 pm: 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
Title: Re: possible issue with capping interaction
Post by: auffinger on February 15, 2015, 10:32:58 am: 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
Title: Re: possible issue with capping interaction
Post by: xiangjun on February 15, 2015, 12:08:35 pm: You can remove the offset by specifying the option --polygon-offset=0. The default is 0.27 A.

HTH,

Xiang-Jun