Messages

1

General discussions (Q&As) / Re: plot to show DNA conformation

« on: March 07, 2013, 06:53:33 am »

BS"D

Dear Xiang-Jun,

  Thanks for the reply.  It turns out that the PDB validation server also does some analyses (NUCHECK), and gives several different kinds of plots, one of which is based on your algorithm for base morphology comparison.  Another one is a scattergram of torsion angles.  What I want to compare is actually not so drastic as A to B conversion, rather B to modified B upon protein binding.  So I will have to see which parameters allow me to reliably discriminate the changes.
 
Thanks for the info...

Harry

2

General discussions (Q&As) / plot to show DNA conformation

« on: March 06, 2013, 07:55:39 am »

BS"D

Dear All,

  I would like to create a plot along the lines of protein Ramachandran plot, where one could see changes in the conformation of the DNA.  So one could look at the plot and see that the ds DNA was ideal B DNA, or perhaps A DNA, or something else.  I want to see how a given stretch of ds DNA changes during an MD simulation, and whether it goes from one type to another.   Couldn't really see a previous example of this in the manual....

Thanks

Harry