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Author Topic: x3dna-dssr installation  (Read 679 times)

Offline thanhlequoc

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x3dna-dssr installation
« on: March 22, 2017, 08:29:45 pm »
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"

Offline xiangjun

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Re: x3dna-dssr installation
« Reply #1 on: March 22, 2017, 09:01:42 pm »
Hi,

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

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

shows that the software has been installed properly.

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

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: [Select]
pwd
which x3dna-dssr
echo $PATH

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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline thanhlequoc

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Re: x3dna-dssr installation
« Reply #2 on: March 22, 2017, 09:06:26 pm »
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

Offline xiangjun

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Re: x3dna-dssr installation
« Reply #3 on: March 22, 2017, 09:32:57 pm »
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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline thanhlequoc

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Re: x3dna-dssr installation
« Reply #4 on: March 27, 2017, 05:35:31 pm »
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

Offline xiangjun

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Re: x3dna-dssr installation
« Reply #5 on: March 27, 2017, 08:07:24 pm »
Quote
I was able to run x3dna-dssr after following your advice. Thank you very much!

Glad to hear the installation problem has been solved. From the above info, it's hard to guess what route you took. By design, it should be straightforward to get DSSR up and running. That's been the case in my experience over the past few years. Your scenario worths attention for the benefit of other new DSSR users. Could you please detail how you solve the DSSR installation problem, step-by-step, from a beginner's perspective?

Quote
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.

This question has nothing to do with the current topic on "x3dna-dssr installation". Please start a new thread.

Hopefully, I've made my points clear.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline thanhlequoc

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Re: x3dna-dssr installation
« Reply #6 on: March 27, 2017, 10:16:28 pm »
X3DNA-DSSR installation
1) Install x3dna following the steps indicated by Dr. Xiangjun.
2) Download x3dna
3) On Mac OS X or Linux, run the command ‘chmod u+x x3dna-dssr’ to make DSSR executable.
4) Since the path is already set for x3dna, drag x3dna-dssr to the bin folder located in x3dna folder.
5)./x3dna-dssr -h to confirm the installation.

Offline xiangjun

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Re: x3dna-dssr installation
« Reply #7 on: March 27, 2017, 10:56:50 pm »
Note: DSSR is fully self-contained, and independent of 3DNA v2.3. DSSR (the x3dna-dssr executable) does not need to be in the $X3DNA folder at all. It can be put anywhere in your PATH, as documented in the User Manual.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.