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Author Topic: DSSR output path  (Read 9782 times)

Offline KerstinRe

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DSSR output path
« 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

Offline xiangjun

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Re: DSSR output path
« Reply #1 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

 

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.