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General discussions (Q&As) / Re: x3dna-v2.3 no backbone ribbon
« Last post by cllawson on July 31, 2018, 12:36:21 pm »
also, for structures with both protein and nucleic acid, no ribbon is appearing for the protein.
12
General discussions (Q&As) / x3dna-v2.3 no backbone ribbon
« Last post by cllawson on July 31, 2018, 12:28:39 pm »
Hi Xiang-Jun,

I have been trying to replicate the images that appear on NDB using your latest x3dna package (v2.3) on Mac OS. 

When i run blocview filename.pdb, I get the message:

cannot find 'render'
no image output; 'blocview.r3d' -- to be fed into render/pymol

Which is fine because I have MacPymol so I can view/snap images of the r3d file. 

However, the images I get do not include the backbone ribbon, even though it seems it should be the default to include it (blocview --help states that --no-ds turns it off), so this seems like a bug.

I've attached an example image.

Thanks in advance for your help!
13
FAQs / Re: How to set up 3DNA on Windows
« Last post by xiangjun on July 30, 2018, 11:37:13 pm »
Hi,

You do not need ConEmu to run 3DNA, even though ConEmu is a much better command-line interface than the native cmd.exe on Windows. Moreover, ConEmu has nothing to do with importing PDB files.

Please follow the steps and show us where you got stuck, preferrable with screenshots.

Best regards,

Xiang-Jun
14
FAQs / Re: How to set up 3DNA on Windows
« Last post by xiaoxuesheng on July 30, 2018, 10:17:19 pm »
Dear XiangJun,
I've configured the environment variables and they're correct, but there won't be ConEmu, and I don't know the basic problem of how ConEmu imports a PDB file.
Can you give me a tutorial on how to use it? Do you have a visual action window, if any, where to use it?
I'm using windows.Thanks.
15
Web-DSSR / Web DSSR for dissecting the spatial structures of nucleic acids
« Last post by shuxiang on July 29, 2018, 02:16:30 pm »
Web DSSR is a user-friendly web-based interface for analyzing and visualizing three-dimensional (3D) nucleic-acid-containing structures. The server allows the user to determine a wide variety of conformational parameters in a given PDB ID or uploaded structure. Meanwhile, the secondary structure visualization component offers simultaneously highlighting of 1D, 2D, and 3D nucleic-acid structures.

The wDSSR web server is located at http://web.x3dna-dssr.org/.

Any questions and bug reports are welcome!

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It should be possible. RNAstructure or ViennaRNA package may already have some utility, or you may need to write some code to parse the DBN to get what you want. As mentioned before, DSSR do not have such functionality.

Best regards,

Xiang-Jun
17

Hello,
yes it is right. I just want to generate an excel file telling me exactly the number of nucleotides per helices to do some statistic. Do you think it is possible?
thanks
18
Hi,

It is not completely clear to me what you want to achieve, based on the information provided. However, DSSR is unlikely to be the tool you are looking for since DSSR takes a 3D structure as its starting point.

If you already have the 2nd structure in dot-bracket notation (DBN), I’d assume the nucleotides in matached () are involved in helices. Right?

Xiang-Jun
19
Hello,
I have determined reactivities of approximately 2000 nucleotides of several RNA samples using SHAPE and generated dot bracket files. I am able to fold RNAs using these reactivities using RNA structure but I also would like to automatically determine the position and the number of nucleotides involved in helices. Is it possible to do this type of analysis with a software?

thanks for your help
20
RNA structures (DSSR) / Re: List only base pairs in output
« Last post by Llewellyn on July 26, 2018, 01:41:41 pm »
Thanks. It worked!
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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.