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Author Topic: Identify sugar type in the DSSR output  (Read 251 times)

Offline brinda.vallat

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Identify sugar type in the DSSR output
« 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"............}]


Offline xiangjun

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Re: Identify sugar type in the DSSR output
« Reply #1 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

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

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Offline brinda.vallat

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Re: Identify sugar type in the DSSR output
« Reply #2 on: April 24, 2020, 10:42:39 am »
Great! Thank you very much. I will use the updated version and get back to you.

Offline brinda.vallat

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Re: Identify sugar type in the DSSR output
« Reply #3 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], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.