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Author Topic: possible issue with capping interaction  (Read 4372 times)

Offline Auffinger

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possible issue with capping interaction
« 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
pascal auffinger
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Offline xiangjun

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Re: possible issue with capping interaction
« Reply #1 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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline Auffinger

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Re: possible issue with capping interaction
« Reply #2 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
pascal auffinger
ibmc-cnrs
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Offline xiangjun

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Re: possible issue with capping interaction
« Reply #3 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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.