possible issue with capping interaction

[auffinger]

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

[xiangjun]

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

[auffinger]

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

[xiangjun]

You can remove the offset by specifying the option --polygon-offset=0. The default is 0.27 A.

HTH,

Xiang-Jun