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Questions and answers > RNA structures (DSSR)

x3dna-dssr installation

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thanhlequoc:
Hi Dr. Xiangjun,
I am trying to install x3dna-dssr to my mac; I had successfully installed x3dna. However, I am having trouble to run the program. Using the command line "x3dna-dssr -h" only gives me command not found. Futhermore, double-clicking on the icon, it gives me this
missing required option: must specify -i=PDBFile/mmCIF
type: 'x3dna-dssr -h' for help
What should I do?
Thanks,
Thanh Le
P.S. After downloading x3dna-dssr from the website, I moved it to a bin folder and used the command "chmod u+x x3dna-dssr"

xiangjun:
Hi,

Thanks for using DSSR. The message when you double-clicked on the icon:


--- Quote ---missing required option: must specify -i=PDBFile/mmCIF
--- End quote ---

shows that the software has been installed properly.


--- Quote ---Using the command line "x3dna-dssr -h" only gives me command not found.
--- End quote ---

This error message shows that the DSSR executable (x3dna-dssr) is not in your PATH. Could you report back what you get with the following commands:


--- Code: ---pwd
which x3dna-dssr
echo $PATH
--- End code ---

If you know exactly the bin/ folder where DSSR is installed, you can always use the full path to specify the DSSR command.

Xiang-Jun

thanhlequoc:
Thank you for the quick response.
Here is the response from terminal:
thanhs-MacBook-Pro-2:bin ThanhLe$ pwd
/Users/ThanhLe/desktop/bin
thanhs-MacBook-Pro-2:bin ThanhLe$ which x3dna-dssr
thanhs-MacBook-Pro-2:bin ThanhLe$ echo $PATH
/Users/ThanhLe/Desktop/x3dna-v2.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
Please advice.
Thanks,
Thanh Le

xiangjun:
You're in "/Users/ThanhLe/desktop/bin" (pwd), the empty output from "which x3dna-dssr" shows the command is not in your PATH. The "echo $PATH" shows you have "/Users/ThanhLe/Desktop/x3dna-v2.3/bin" in your PATH.

So you could move the executable "x3dna-dssr" from its installation directory to /Users/ThanhLe/Desktop/x3dna-v2.3/bin by drag-and-drop.

If you've installed x3dna-dssr in the "/Users/ThanhLe/desktop/bin" folder, and you're in that folder, you could run it as "./x3dna-dssr -h".

HTH,

Xiang-Jun

thanhlequoc:
Hi Dr. Xiangjun,
I was able to run x3dna-dssr after following your advice. Thank you very much!
I have a quick question about hydrogen bonds-can the program find hydrogen bonds between protein and rna (a docked system)? I have tried using get-hbonds command. However, it only gives me hydrogen bonds in rna-not between protein and rna.
Thanks,
Thanh Le

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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.