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Questions and answers => RNA structures (DSSR) => Topic started by: brinda.vallat on April 23, 2020, 01:38:19 pm

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Title: Identify sugar type in the DSSR output
Post by: brinda.vallat on April 23, 2020, 01:38:19 pm
It would be useful if DSSR output can provide information regarding the sugar type for each nucleotide i.e., whether the sugar is ribose or deoxyribose.

For example, in the JSON output, there can be a new item within the "nts" object that provides this information:

"nts":[{"index":1,"index_chain":1,"chain_name":"N","nt_resnum":24,"nt_name":"A","nt_code":"A","nt_id":"1..N.A.24.", "nt_sugar_type":"ribose"............}]

Title: Re: Identify sugar type in the DSSR output
Post by: xiangjun on April 23, 2020, 02:39:19 pm
I've just updated DSSR to v1.9.10-2020apr23. It has a new field named "nt_type", with possible values of "DNA", "RNA" or "unknown". Since the item is included in the nts[] array, I've used the name "nt_type" instead of your suggested "nt_sugar_type" (with values of "ribose" or "deoxyribose" etc).

Please download the updated DSSR (forget about the label, which still reads "v1.9.9-2020feb06"), and report back how it goes.

Best regards,

Xiang-Jun

Title: Re: Identify sugar type in the DSSR output
Post by: brinda.vallat on April 24, 2020, 10:42:39 am
Great! Thank you very much. I will use the updated version and get back to you.
Title: Re: Identify sugar type in the DSSR output
Post by: brinda.vallat on April 24, 2020, 11:11:04 am
I downloaded and tested the updated DSSR version. It works very well. Thank you!

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.