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Author Topic: Support for batch processing?  (Read 1997 times)

Offline Walker

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Support for batch processing?
« 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?

Offline xiangjun

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Re: Support for batch processing?
« Reply #1 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


« Last Edit: March 10, 2020, 04:46:58 pm by xiangjun »

Offline xiangjun

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Re: Support for batch processing?
« Reply #2 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 has more advanced features and much better usability than 3DNA, including such batch processing.

Xiang-Jun
« Last Edit: March 06, 2021, 02:36:39 pm by xiangjun »

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.