3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: Walker on March 10, 2020, 01:54:27 pm

Title: Support for batch processing?
Post by: Walker on March 10, 2020, 01:54:27 pm: Hello,

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?
Title: Re: Support for batch processing?
Post by: xiangjun on March 10, 2020, 02:02:31 pm: Hi,

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,

Xiang-Jun
Title: Re: Support for batch processing?
Post by: xiangjun on March 06, 2021, 11:55:44 am: Hi,

Quote
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?

You may have already found a solution to the above question. As a follow-up, the fiber module in DSSR Pro (http://innovation.columbia.edu/technologies/CU20391) has more advanced features and much better usability than 3DNA, including such batch processing.

Xiang-Jun