Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Author Topic: Support for batch processing?  (Read 394 times)

Offline Walker

  • with-posts
  • *
  • Posts: 1
    • View Profile
Support for batch processing?
« on: March 10, 2020, 01:54:27 pm »

I'm using the 'fiber' command in a local installation of 3DNA to generate DNA structures from specified sequences in .pdb format for use in subsequent simulations. However, I would like to generate separate .pdb files for thousands of unique DNA sequences.

Is there a way to use this command on a batch of sequences to generate separate .pdb files for each sequence without manually entering each sequence into the command line?

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1524
    • View Profile
    • 3DNA homepage
Re: Support for batch processing?
« Reply #1 on: March 10, 2020, 02:02:31 pm »

You could use file redirections for batch process. Or try other available tools that may be able to do this job better. If I could receive continued funding support, I will improve the 3DNA "fiber" command for applications like this. Nowadays, such feather enhancements are treated as "incremental" (not "novel"), and I may no longer be able to continuously support the community.

Best regards,


« Last Edit: March 10, 2020, 04:46:58 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]

* Click "NOTIFY" to receive email notifications
* Original Poster, please provide a summary
* DSSR 2.0 has superseded the 3DNA v2.4 suite


Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.