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Questions and answers => RNA structures (DSSR) => Topic started by: KerstinRe on November 17, 2014, 09:14:28 am

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Title: DSSR output path
Post by: KerstinRe on November 17, 2014, 09:14:28 am

Dear Xiang-Jun,

I have a question concerning the DSSR output path. How can I give the output path for the „additional files“ (dssr-torsions.txt etc.). I use the following command line:

x3dna-dssr -i=/Users/.../3DNA/1OCT.pdb -o=/Users/.../3DNA/1OCT_dssr.out

But the additional files are all saved in my home directory. I would like to save them together with 1OCT_dssr.out.

Thanks in advance!

Best regards
Kerstin

Title: Re: DSSR output path
Post by: xiangjun on November 17, 2014, 11:58:40 am

Hi Kerstin,

By design, the default files are put in the directory where x3dna-dssr is run. In your case, it seems you are running DSSR from your home directory, and that's why all the dssr-*.* files are directed there. To get the auxiliary files together with the main DSSR output file, switch to the directory where you want to put all the files. Suppose you have '1msy.pdb' in ~/tmp/dssr-run/1msy.pdb, then you can do:

Quote

cd ~/tmp/dssr-run/; x3dna-dssr -i=1msy.pdb -o=1msy.out

You may want to put directory switching in a script for batch processing of many PDBx/mmCIF or PDB files.

HTH.

Xiang-Jun

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