Messages

1

General discussions (Q&As) / Re: calculate step parameters of a funny step

« on: July 24, 2008, 12:35:12 pm »

Hi! Xiangjun:
Thanks! I changed the setting of misc_3dna.par so that 3dna does not recognize the step 57 as a breakage of helices. Everything works fine now.

Best,

Fei

2

General discussions (Q&As) / calculate step parameters of a funny step

« on: July 23, 2008, 10:54:49 am »

HI! Xiangjun:
I can't get the values of step parameters of step 57 in the pdb file attached here (2f8n.pdb). I checked the 3D-structure. The base pair 58 (58 G and 233 C) in dimer step 57 is a funny base pair, whose Propeller is -60 degree ( I attach a picture of step 57). I guess, 3DNA might put some constrains to base pairs so that I can't get the value of step parameters of step 57. How can I avoid the constrains and get the values of the step parameters

Thanks!

Best,

Fei

3

General discussions (Q&As) / the center of a dimer step

« on: September 29, 2006, 01:53:02 pm »

HI! Xiangjun:
In which file among the 3DNA output files can I find the center of a dimer step?
Thanks a lot!
Fei