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Author Topic: Identify sugar type in the DSSR output  (Read 20513 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


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!

 

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University