3DNA Forum

Questions and answers => MD simulations => Topic started by: maryatx3dna on July 25, 2015, 03:55:43 am

Netiquette · Download · News · Gallery · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Video Overview · DSSR v2.5.2 (DSSR Manual) · Homepage

Title: base overlap
Post by: maryatx3dna on July 25, 2015, 03:55:43 am

Sir,

is there any way i could extract the stacked base overlap area as a function of time?
could i extract overlap area in analysis o/p

Title: Re: base overlap
Post by: xiangjun on July 25, 2015, 09:34:41 am

Will the Ruby script x3dna_ensemble distributed with 3DNA do the trick?

Alternatively, you may want to get do_x3dna (http://bioinformatics.oxfordjournals.org/content/early/2015/04/01/bioinformatics.btv190.abstract) a try.

HTH,

Xiang-Jun

Title: Re: base overlap
Post by: maryatx3dna on July 26, 2015, 11:39:16 am

ok sir

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