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Questions and answers => General discussions (Q&As) => Topic started by: bala on February 13, 2007, 04:30:21 am

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Title: using 3dna to analyze quadruplex
Post by: bala on February 13, 2007, 04:30:21 am

Hello,

I am using 3DNA to analyze a quadruplex structure.  I gave the command as follows,

find_pair -pt quad.pdb quad.bps | anyhelix.  

It created the following files
mulbp.inp, mref_frames.dat, allpairs.pdb, ref_frames.dat etc.

I want to calculate the backbone torsions and pucker.  But i am not finding these informations in any file. I doubt whether it is possible to calculate these values for quadruplex using X3DNA.

Bala

Title:
Post by: xiangjun on February 13, 2007, 08:25:04 pm

Hi,

Regarding applying 3DNA to quadruplex, you might find this post in the forum relevant (http://http://3dna.rutgers.edu:8080/forum/viewtopic.php?t=13).

If your are only interested in calculate the backbone torsions and pucker of any nucleic acid structure, the following command will do the trick:

Code: [Select]

find_pair -s -t PDB_FILE stdout | analyze

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