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Questions and answers => General discussions (Q&As) => Topic started by: auffinger on April 17, 2010, 01:19:28 pm

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Title: non planar base pairs
Post by: auffinger on April 17, 2010, 01:19:28 pm
Dear Xiang-Jun,

Another interrogation related to 3DNA. We came accross a strange base pair selected by find_pair, the base looks almost othogonal and this, although not frequent, is not a unique case (this base pair involves symmetry related residues). We used find_pair -p on a modified PDB file of the 1DC0 structure with following parameters:
Base-pair criteria used:   3.35   0.00  15.00   1.50  65.00   4.50   7.50 [ O N].

In which way should we change these parameters in order to eliminate such base pairs (thought stagger=1.5 would do)?

see attached files,

Best regards,

Pascal
Title: Re: non planar base pairs
Post by: xiangjun on April 17, 2010, 09:44:02 pm
Hi Pascal,

This is clearly posed question.

In file "misc_3dna.par", there is the following section:

Code: [Select]
#   maximum angle between base normals (in range 0..90)
<max_plane_angle>65.0</max_plane_angle>
In your specific case, setting the number from the default 65.0 degrees to 60.0 will solve your problem.

For more details, please see FAQ "How to fix missing (superfluous) base pairs identified by find_pair?" (http://http://3dna.rutgers.edu/x3dna/faqs#find_pair)

[hr:2mhasqib][/hr:2mhasqib]
Furthermore, in our recent GpU paper (http://http://nar.oxfordjournals.org/cgi/content/full/gkq155) (see also my blog post: "What's special about the GpU dinucleotide platform?" (http://http://xiang-jun.blogspot.com/2010/04/whats-special-about-gpu-dinucleotide.html)):

Quote
We chose the following set of stringent parameters to ensure that the geometry of each identified base pair is nearly planar and supports at least one inter-base H-bond: (i) a vertical distance (stagger) between base planes ≤1.5 Å; (ii) an angle between base normal vectors ≤30°; and (iii) a pair of nitrogen and/or oxygen base atoms at a distance ≤3.3 Å.
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.