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

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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


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.