Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Author Topic: 3DNA Cannot find help3dna.dat  (Read 6064 times)

Offline slaw

  • with-posts
  • *
  • Posts: 19
    • View Profile
3DNA Cannot find help3dna.dat
« on: September 06, 2011, 05:44:28 pm »

I downloaded 3DNA v2.0 and have installed it on a Linux machine.  However, upon executing find_pair I get the error:

open_file </home/seanlaw/X3DNA/config/help3dna.dat> failed: No such file or directory

Of course, find_pair is installed in:


I'm not sure why find_pair is trying to look in that particular directory and what I can/need to do to have find_pair look in



Any help or suggestions would be greatly appreciated.  Thanks


P.S.  I tried searching for help3dna.dat but found nothing.

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1642
    • View Profile
    • 3DNA homepage
Re: 3DNA Cannot find help3dna.dat
« Reply #1 on: September 06, 2011, 09:58:47 pm »
Hi Sean,

It is likely that you've not properly set up 3DNA v2.0. Did you run [red:1nrkjhgd]x3dna_setup[/red:1nrkjhgd] as documented in the 2008 3DNA Nature Protocols paper?

More specifically, what's the output from running the following:
Code: [Select]
echo $X3DNABy default, if the [mono:1nrkjhgd]X3DNA[/mono:1nrkjhgd] environment variable is not set, the program will use [mono:1nrkjhgd]$HOME/X3DNA[/mono:1nrkjhgd]. That explains the error message:
[pre:1nrkjhgd]open_file </home/seanlaw/X3DNA/config/help3dna.dat> failed: No such file or directory[/pre:1nrkjhgd]



Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.