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Questions and answers => RNA structures (DSSR) => Topic started by: dunbrack on June 18, 2020, 05:57:43 pm

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Title: 3DNA/DSSR download issue
Post by: dunbrack on June 18, 2020, 05:57:43 pm

I tried to download the latest version of 3DNA. But there are no extensions on the files (they are all "x3dna-dssr") and it is not clear what format they are. I tried .dmg extension for the Mac version and .tar, .tar.gz and .zip for the Linux versions. None of them opened. What are they?

Thanks,
Roland
roland.dunbrack@fccc.edu

Title: Re: 3DNA/DSSR download issue
Post by: xiangjun on June 18, 2020, 06:30:47 pm

Dear Roland,

Thanks for your interest in DSSR. The binary file x3dna-dssr is all it is. Assuming you have downloaded the macOS or Linux version, simply run "chmod +x x3dna-dssr" to make it executable. Then you're all set. By design, the simplicity with DSSR is out of the norm. One may even feel it anticlimactic in the big data, bloated software era.

Check with "x3dna-dssr -h" for further information. See the DSSR User Manual for details (http://docs.x3dna.org/dssr-manual.pdf). If you have any further questions, please do not hesitate to ask.

Best regards,

Xiang-Jun

Title: Re: 3DNA/DSSR download issue
Post by: xiangjun on June 20, 2020, 12:23:58 pm

As a follow-up of my previous response, I would like to clarify the following points:

• The binary executables of DSSR is named x3dna-dssr in macOS and Linux, and x3dna-dssr.exe in Windows, per conventions in the Unix-like and Windows operating systems.
• After downloading x3dna-dssr in macOS and Linux, users should run chmod +x x3dna-dssr to set the execute permission. The x3dna-dssr file at the download site actually has this execute permission; for security reasons, it is switched off during the downloading process.
• The binary executable of DSSR is < 2MB. It is completely self-contained. No hundreds of MB even GB of a download to un-package/install; no configurations; no dozens of dependencies. Such complicated things users may get used to nowadays simply do no exist in DSSR.
• Getting DSSR up and running has never been an issue over the past eight years, even (especially) with beginners. The instruction given here should be sufficient for the majority of users to get started with DSSR. The DSSR User Manual  (http://docs.x3dna.org/dssr-manual.pdf)contains detailed installation instructions and common usages. The manual is well worth reading not only for DSSR users but also for those interested in nucleic acid structural bioinformatics.

Best regards,

Xiang-Jun

Title: Re: 3DNA/DSSR download issue
Post by: leagrille on September 07, 2020, 08:46:04 am

Hello! I 've submitted license requests for downloading Dssr several times, but i've never been contacted by Columbia University.  Is there any other way of getting dssr 2.0? Thank you-

Title: Re: 3DNA/DSSR download issue
Post by: xiangjun on September 07, 2020, 10:20:34 am

Hi,

Thanks for your interest in using DSSR 2.0, and for posting the questions on the 3DNA Forum. Without details, however, I cannot offer further help.

DSSR v2.0 is licensed by Columbia University, and it is only available from the Columbia Technology Ventures (CTV) website (http://innovation.columbia.edu/technologies/CU20391). From what I heard, the CTV has been responsive to legitimate requests for the three types of DSSR licenses.

Best regards,

Xiang-Jun

Title: Re: 3DNA/DSSR download issue
Post by: yaromnix on November 18, 2020, 01:12:27 am

Hello,
Not seeing any "Downloads" forum section after registration and activation. No longer available to academic users?

Title: Re: 3DNA/DSSR download issue
Post by: xiangjun on November 18, 2020, 11:19:09 am

Hi,

You should be able to see the "Downloads" section now.

As of v2.0, DSSR is licensed by Columbia University, and it is only available from the Columbia Technology Ventures (CTV) (http://innovation.columbia.edu/technologies/CU20391) website.

Best regards,

Xiang-Jun

Title: Re: 3DNA/DSSR download issue
Post by: naoto on April 13, 2021, 02:09:21 pm

Hello,

Is it correct that the source code of x3dna is no longer available even after agreeing to the CTV licence?

Title: Re: 3DNA/DSSR download issue
Post by: xiangjun on April 13, 2021, 03:43:40 pm

Hi,

The source code of 3DNA v2.4 is available for academic users from this Forum. You should see the "Downloads" page after verification of your registration email. DSSR is licensed by CTV, and is distributed in binary executable forms only.

Xiang-Jun

Title: Re: 3DNA/DSSR download issue
Post by: naoto on April 13, 2021, 05:00:29 pm

Thank you Xiang-Jun.

Somehow I could not see Download under the Welcome tab this morning, even after logging in with my account. But now I see the download page.

I appreciate you leave the code available.
Naoto

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.