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Author Topic: using 3dna to analyze quadruplex  (Read 9699 times)

Offline bala

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using 3dna to analyze quadruplex
« 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

Offline xiangjun

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« Reply #1 on: February 13, 2007, 08:25:04 pm »
Hi,

Regarding applying 3DNA to quadruplex, you might find this post in the forum relevant.

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

 

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.