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Questions and answers => General discussions (Q&As) => Topic started by: kgulati on February 19, 2007, 04:16:24 pm

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Title: Backbone torsions
Post by: kgulati on February 19, 2007, 04:16:24 pm

Hello,

I have been using 3DNA with the find_pair tool and was wondering if it is possible to determine backbone torsion parameters for all of the residues within a PDB.  As I am using it now it only finds the parameters for the residues in each pair found by find_pair.

Thanks.

Title:
Post by: xiangjun on February 19, 2007, 11:24:57 pm

Yes, there is a way in 3DNA to calculate all backbone torsion angles of any nucleic acid structure in PDB format. It is as follows:

Code: [Select]

find_pair -s -t PDBFILE stdout | analyze

where option "-s" (or equivalently "-1") is used to treat the whole structure  as a continuous single helix,  needed for getting all backbone torsion angles.

The "-t" option also takes consideration of HETATM records for modified bases. Note that in the coming new release of 3DNA v2.0, "-t" will be set by default, thus it will no longer be needed.

Of course, this method assumes that the nucleotides in the PDB structure are in proper order in the 5'-->3' direction. This should normally be the case. If need arises, I will consider add a new functionality in "find_pair" to make the  nucleotides in order no matter whatever their original positionings in the PDB file are.

HTH,

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University