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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
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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:
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.