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DSSR Download Issue
received a license approval to download DSSR- Basic and when I downloaded, I received an error. The software is still not working (see screenshot). Please advise how I can fix.
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Thanks for your interest in using DSSR. Your screenshot provides information that explains why you're having problems using DSSR.
You're on a macOS, and you have double-clicked the x3dna-dssr executable to run it. I can reproduce your case by installing x3dna-dssr under the ~/Downloads folder and double-clicking it. The error message is quite informative, by showing that x3dna-dssr is run, and immediately exit. Running x3dna-dssr without any options gives the following message:
missing required option: must specify -i=PDBFile/mmCIF
type: 'x3dna-dssr -h (or --help)' for further help
'x3dna-dssr --citation' for preferred citation(s)
Time used: 00:00:00:00
That means DSSR is already successfully installed on your macOS. It is just that DSSR is a command-line (CLI) program, and you need a terminal window to run it. There are many online tutorials on how to get started using terminal on macOS. Here is one: Absolute BEGINNER Guide to the Mac OS Terminal (https://www.youtube.com/watch?v=aKRYQsKR46I&t=11s). Once you are familiar with the terminal, running DSSR should be straightforward, as detailed in the User Manual.
The DSSR executable (x3dna-dssr for macOS and Linux, and x3dna-dssr.exe for Windows) is self-contained and does not rely on any third-party libraries. There is no need for any setup or configurations: type x3dna-dssr -h to verify your installation. Note that DSSR is a command-line program: you need a terminal window to run it.
If you're GUI-driven and do not want to use CLI at all, then you may find the following two resources helpful:
- DSSR-enabled Innovative Schematics of 3D Nucleic Acid Structures with PyMOL (http://skmatics.x3dna.org)
- Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures (http://web.x3dna.org)
Best regards,
Xiang-Jun
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As a follow up, please note that:
The CTV distributes DSSR Basic and Pro versions in zip format for macOS, Linux, and Windows. Each zip file contains a DSSR binary executable as well as the associated user manual.
Assuming basic command-line knowledge, users should be able to follow the instructions in the manual and reproduce reported results.
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