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Questions and answers => General discussions (Q&As) => Topic started by: satary on April 03, 2015, 07:05:20 am

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Title: x3dna rebuild and standard input
Post by: satary on April 03, 2015, 07:05:20 am

Hello!
Thanks a lot for a great software !
I've found that rebuild utility accepts 'stdin' option for input e.g.
cat custom_step.par | rebuild -atomic stdin gorgeous_structure.pdb
But it always fails with :
"error reading parameter file: step or helical option"
but rebuild -atomic custom_step.par gorgeous_structure.pdb works just fine
Am I doing something wrong or is that a bug?

Thank you!

Title: Re: x3dna rebuild and standard input
Post by: xiangjun on April 03, 2015, 11:52:39 am

Hi,

Quote

Thanks a lot for a great software !

Thanks for using 3DNA and for your nice words about the software.

Quote

I've found that rebuild utility accepts 'stdin' option for input e.g.
cat custom_step.par | rebuild -atomic stdin gorgeous_structure.pdb
But it always fails with :
"error reading parameter file: step or helical option"
but rebuild -atomic custom_step.par gorgeous_structure.pdb works just fine
Am I doing something wrong or is that a bug?

I can reproduce the problem you reported here. You may take it as a bug or inconsistency in 3DNA's handling of 'stdin' input. Internally, the parameter input file is read twice: the first time for the number of base pairs to allocate the data structure, and the second time to fill in the contents. That's why 'stdin' does not work. I will try to fix this issue in the coming release of 3DNA v2.2. In the meantime, just remember to always use an explicit parameter file.

Xiang-Jun

Title: Re: x3dna rebuild and standard input
Post by: satary on April 04, 2015, 07:14:37 am

Thank you for quick respond, I'll be aware!
Looking forward for an update!

Title: Re: x3dna rebuild and standard input
Post by: xiangjun on April 10, 2015, 05:31:20 pm

Hi,

I've updated 3DNA to v2.2 which fixes this problem. Please download it and have a try. Report back any issue you may still have.

Xiang-Jun

Title: Re: x3dna rebuild and standard input
Post by: satary on November 09, 2015, 06:22:30 am

Thank you! That works great!

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University