3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: Andrea R on September 10, 2022, 06:48:52 pm

Title: Calculate torsion angles of the DNA, without taking into account the bases
Post by: Andrea R on September 10, 2022, 06:48:52 pm: Dear Dr. Xiang-Jun Lu,

I used versions of 3DNA earlier than the 2018 versions some time ago, in those versions it was possible to calculate the torsion angles of the sugar-phosphate backbone of DNA, without taking into account the bases, with the following command:

analyze -t = name.tor name.pdb

However in the new versions, this task is not possible anymore, it is necessary to have the nitrogenous bases or at least N1, C2 or N9, C4 atoms.

I was wondering if there is a new instruction or way to do that, because it would shorten my work route considerably. One of my study purposes is the optimized fragments of the Sugar-Phosphate Backbone, in these fragments the nitrogenous bases of the DNA are eliminated and replaced by a hydrogen (position N1 or N9) as shown in file attached .

Thank you very much,

Andrea R.
Title: Re: Calculate torsion angles of the DNA, without taking into account the bases
Post by: xiangjun on September 10, 2022, 09:38:10 pm: Hi Andrea,

DSSR Pro can do what you want very easily, especially in combination with the --json option. See No more grant funding for 3DNA/DSSR (http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/).

Base atoms have always been necessary for the identification of nucleotides in order to calculate base-pair and backbone parameters in 3DNA v2.x, including the command you mentioned: analyze -t=torsions.out. However, since 3DNA v2.x is open source for academic uses, you can modify it to meet your needs.

Best regards,

Xiang-Jun