Messages

1

RNA structures (DSSR) / Re: global bending of a single stranded DNA

« on: July 18, 2016, 05:34:17 pm »

Hi Xiang-Jun,

thank you for your reply.
As example, in the case of a double stranded DNA, I was calculating some global parameters like the Total bend , Helical-rise and Helical-Twist.
Of course , since a helix is not present in a double stranded DNA, the Helical-rise and Helical-Twist are not meaningful.
However, for a single stranded DNA, the global bent would be a very useful parameter. Is it possible to have a measure of it using DSSR? If not, can you suggest me some other measures

It is very important for my topic. I need to understand how the motions of my single strand correlate with the other part of the system.
any suggestion is welcomed!

anyway, I am a big fan of 3DNA and now of DSSR too!

many thanks
Giulia



 

2

RNA structures (DSSR) / global bending of a single stranded DNA

« on: July 18, 2016, 04:30:33 pm »

Dear Xiang-Jun Lu,


I have used extensively 3DNA during my work and I am now exploring DSSR.

I am successfully using it for the analysis of a single-strand DNA, for which I can obtain correctly the backbone parameters.

However, I am interested in calculating the global bending of the steel. This , I have not be able to do.

Is it possible with your code? could you please give me some advises?

Thank you very much
Giulia