Messages

1

General discussions (Q&As) / Re: Intrinsic Curvature of DNA

« on: June 23, 2015, 08:22:47 pm »

Thanks for your reply.
I created the .par file on a Windows machine but use the 3DNA application on a Mac. I think all the original issues are fixed now.
Thank you again for all your help!
Lara

2

General discussions (Q&As) / Re: Intrinsic Curvature of DNA

« on: June 03, 2015, 08:23:06 pm »

I have attached the file. Thank you for your help!

3

General discussions (Q&As) / Re: Intrinsic Curvature of DNA

« on: June 03, 2015, 07:04:34 pm »

Hello again,

I followed the steps using VMD, but when I try to "rebuild" on 3DNA I get "error reading P xyz index".
How can I fix this?

Thanks in advance,
Lara

4

General discussions (Q&As) / Re: Intrinsic Curvature of DNA

« on: June 02, 2015, 02:17:10 pm »

Thank you for your advice, I will try this soon!
Lara

5

General discussions (Q&As) / Re: Intrinsic Curvature of DNA

« on: May 19, 2015, 02:41:00 pm »

Thank you for your quick reply!
Lara

6

General discussions (Q&As) / Intrinsic Curvature of DNA

« on: May 19, 2015, 02:04:21 pm »

Hello,

Thank you for this great program and helpful forum.

Does 3DNA account for the intrinsic sequence dependent curvature of DNA? For example, when I use the reconstruction tool on w3DNA, an A-tract sequence gives a straight segment of DNA. I was expecting something more like this, showing curvature:
http://openi.nlm.nih.gov/imgs/512/281/1176013/1176013_gki699f1.png

Also, is there any way to connect the ends of a linear DNA strand to form a circle?

Thank you in advance,
Lara Ibrahim