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Author Topic: nt_ids for residues i+1 and i-1  (Read 18414 times)

Offline brinda.vallat

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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

Offline xiangjun

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Re: nt_ids for residues i+1 and i-1
« Reply #1 on: February 19, 2021, 11:01:07 am »
Hi Brinda,

Thanks for your request for a new feature in DSSR. Without funding support, I am not able to devote time/effort to new features to DSSR Basic other than bug fixes. Further development and user support are thus being committed to DSSR Pro version only.

Best regards,

Xiang-Jun
 
« Last Edit: February 19, 2021, 12:10:23 pm by xiangjun »

Offline brinda.vallat

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Re: nt_ids for residues i+1 and i-1
« Reply #2 on: February 24, 2021, 11:47:56 am »
Thank you, Xiangjun.

We are trying to get the Pro version.

Offline xiangjun

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Re: nt_ids for residues i+1 and i-1
« Reply #3 on: February 24, 2021, 11:57:13 am »
Hi Brinda,

Thanks! Please let me know once you get the DSSR Pro Academic license. We will follow up from there.

I am positive that DSSR Pro users will feel that the software and quality service is worth the price.


Best regards,

Xiang-Jun
« Last Edit: February 24, 2021, 07:43:30 pm by xiangjun »

 

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