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Author Topic: DSSR of 32 bit version  (Read 544 times)

Offline lijun

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DSSR of 32 bit version
« on: August 27, 2019, 05:01:12 pm »
Hi Xiang-Jun,
     The DSSR of the latest version cannot be used on 32 bit OS. I am wondering if you can provide the executable of 32 bit version or the source code.
     Thanks for your help and best,
Jun

Offline xiangjun

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Re: DSSR of 32 bit version
« Reply #1 on: August 27, 2019, 05:21:23 pm »
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32 bit OS

Which OS are you referring to, Windows, Linux, or macOS?

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

Offline lijun

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Re: DSSR of 32 bit version
« Reply #2 on: August 27, 2019, 05:46:04 pm »
Hi Xiang-Jun,
     I am using linux OS (centos 6.9).
     Thanks for your prompt reply.
Jun

Offline xiangjun

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Re: DSSR of 32 bit version
« Reply #3 on: August 27, 2019, 10:20:24 pm »
Hi Jun,

I am curious about the nature of the DSSR 32-bit issue you experienced.

In the thread "Stems of junction structure have only one base pair" you initiated on January 15, 2019, you wrote:

Quote
I am using the newest DSSR to extract the junction structure, but the stems of some junctions have only one base pair...

Do you remember which version of DSSR you used at that time?

In the current thread, you noted that "The DSSR of the latest version cannot be used on 32 bit OS". What DSSR version is this one?

As far as I can remember, the distributed DSSR versions since 2018 have all been of 64-bit for Linux. I am wondering how could you be able to run DSSR in January but not in August? Did you switch a Linux distribution from 64-bit to a 32-bit?

How difficult is it for you to install a Linux 64-bit distribution? It seems to me that Linux 32-bit OS is out of fashion. Indeed, your request for a DSSR version on Linux 32-bit is the first for over one year since 2018.

I used to have access to a Linux 32-bit OS via an external resource. Unfortunately, it is no longer available. If upgrading your Linux to 64-bit is not an option, I will consider installing a local Linux 32-bit OS just to compile DSSR/SNAP for use cases like yours.

Xiang-Jun


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

Offline lijun

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Re: DSSR of 32 bit version
« Reply #4 on: August 28, 2019, 10:52:34 am »
Hi Xiang-Jun,
     Thanks for your reply.
      Previously I used DSSR on my own computer, but now we need to install it on an old server which uses a 32 bit OS.
      If it is too much time and effort for you, we can pull jobs from the server to run locally, posting the results to the server after the jobs finish. However, this will cause slowdowns for users of our server since the jobs can be run very fast on the external server.
     If you can compile a 32 bit version for us, we would appreciate the help, but if it takes you a lot of time, we can find a sub-optimal workaround.
     Thanks again and best regards,
Jun

Offline xiangjun

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Re: DSSR of 32 bit version
« Reply #5 on: August 28, 2019, 11:51:13 am »
Hi Jun,

Thanks for your feedback. I've compiled DSSR (and SNAP) on Ubuntu 16.04 Linux 32-bit, which is available in the normal registration-only download page. Have a try and let me know how it goes.

It is a pleasure to know DSSR is being integrating into your server. Is it convenient to share with us now what your server is about? Some viewers of the Forum may be interested in your work.

Best regards,

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

Offline lijun

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Re: DSSR of 32 bit version
« Reply #6 on: August 28, 2019, 12:23:46 pm »
Hi Xiang-Jun,
     Thank you very much and it is working now.
     We are implementing a web server to predict SHAPE reactivity from RNA 3D structure. Since the 2D structure is necessary to predict the SHAPE profile from a structure, we are using the DSSR module to extract the 2D structure from a 3D structure file. We hope that our server will help users integrate experimental SHAPE data to guide their RNA structure prediction. The 3D Structure-SHAPE Relationship (3DSSR; named similarly to your program) model was previously reported in "Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis".
      Thanks again for your kind help.
Jun

Offline xiangjun

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Re: DSSR of 32 bit version
« Reply #7 on: August 28, 2019, 12:37:44 pm »
Hi Jun,

Glad to hear that the Linux 32-bit version of DSSR is working.

I heard Dr. Shi-Jie Chen talking about 3DSSR at a workshop last year. I am delighted to know that DSSR and 3DSSR are now connected.

Best regards,

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], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.