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Topics - brinda.vallat

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RNA structures (DSSR) / nt_ids for residues i+1 and i-1
« on: February 18, 2021, 03:09:04 pm »
Dear Xiangjun,

Sometimes we are interested in looking at parameters of residues i+1 and i-1, for a given residue 'i' in the JSON output. If mmCIF files are used for the calculation, this information is straightforward. However, when PDB files are used, this is not always easy, especially if there are insertion codes. 

Would it be possible to identify the nt_ids of residues i+1 and i-1 connected by the backbone? This could be included in the "nts" list.

Thank you,
Brinda

2
RNA structures (DSSR) / 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"............}]


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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.