Topics

1

General discussions (Q&As) / 3DNA version 2.0

« on: April 20, 2009, 06:28:56 am »

Hi,

I've read about version 2.0 of 3DNA. (The website works really nice)
This raises some questions:

1. I sent an E-mail to prof.dr. Olson, but I never get a reply, yet I still would like to use 3DNA v2.0 in the future. Help ?
2. What's new in v2.0 ?
      Perhaps this can be added to the topic on 3DNA v2.0

Regards,
Ramon van der Werf
Ph.D. Student at the Radboud University of Nijmegen, The Netherlands

2

General discussions (Q&As) / Rebuilding protonated RNAs with non-canonical basepairs

« on: July 23, 2008, 07:50:16 am »

Hi all,

I am using 3DNA to rebuild RNA helices which are protonated.
To do so, I first build a DNA helix:
fiber -a pdbfile.pdb
subsequently analyze:
find_pair pdbfile.pdb stdout|analyze
Then replace in the parameter files the thymidines by Urdines, and subsequently rebuild using protonated nucleotides to do so.
[Probably there is a fastre way to do so]

My question is the following:
I found 3DNA can handle all basepairs (canonical and non-canonical), the one flaw I discovered is that it cannot handle U-U basepairs.
Can I fix this problem by modifying some file(s) ? Or is it hard-coded into 3DNA ?

Kind regards,
Ramon van der Werf

3

General discussions (Q&As) / Multiple global helical axes in one structure, how to calc?

« on: June 25, 2008, 03:51:40 am »

Hi,

I have a single structure consisting of two helices seperated by some sort of hinge.
The problem is to find the angle between the two helices.
If I look at the [pdbname].out file, which results from
find_pair [pdbname].pdb stdout|analyze
There is not gobal helix axis defined.

What I want is four HETATM lines in the outputfile, defining the begining and the ending of the global helix axis for both helices.
Can I only obtain this by cutting the PDB in parts and then analyze these parts seperately, and append the HETATM lines to the original PDB file ?


Greetings,
Ramon

E.G. structure looks like this (very schematically):


 |--|
 |--| Helix I
 |--|
 /  
 |   | Non-helical hing-area
   /
 |--|
 |--| Helix II
 |--|

I want the angle between helix I and II