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

Author Topic: "Running 3DNA in cygwin64"  (Read 4941 times)

Offline bciezah1

  • with-posts
  • *
  • Posts: 20
  • bciezah1
    • View Profile
"Running 3DNA in cygwin64"
« on: March 16, 2017, 07:41:18 pm »

I am Basilio Cieza. I have a question. I download 3DNA without problems, I download cygwin64 already and I followed the steps you suggested in a previous related question ( which suggest that everything is going well. However, I do not know if the installation was correctly done or not. I try to follow this manual ( but it seems that the commands like "find_pair pde0128.pdb pde0128.inp" are not working. I receive the message the command does not exist when I tried  to run it. I will really appreciate your advice.

Thank you so much,


Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1640
    • View Profile
    • 3DNA homepage
Re: "Running 3DNA in cygwin64"
« Reply #1 on: March 16, 2017, 09:06:02 pm »
Hi Basilio,

Thanks for using 3DNA and for posting your questions on the Forum.

I receive the message the command does not exist when I tried  to run it.

This message means that 3DNA has not been installed properly on your computer. Based on your description, it is hard to guess where the problem could be. Could you provide screenshots showing step-by-step how far you've proceeded? I know your frustrations and would be happy to guide you through the process.

With the help of the x3dna_setup script, getting 3DNA up and running should normally take no more than a few minutes. Over the years, however, I've heard many hard experiences from new users on Windows. That's one of the reasons why I made DSSR and SNAP self-contained, without the setting up step.

Best regards,

« Last Edit: March 16, 2017, 09:13:15 pm by xiangjun »


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