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Questions and answers => RNA structures (DSSR) => Topic started by: cllawson on January 09, 2021, 09:05:52 am

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Title: DSSR eta-base theta-base
Post by: cllawson on January 09, 2021, 09:05:52 am

Dear Xiangjun, 

Wishing you a Happy New Year! 

I have a request regarding DSSR json output for pseudotorsion angles.  I noticed that when backbone is present but no base has been modelled,  eta-base and theta-base values are listed as 0.0 and 0.0. Could you instead assign "null" as done for other pseudotorsion angles that cannot be calculated?  (e.g. eta for 1st residue in a polymer always shows as "null").  PDB ids where I noticed this issue: 6g4s (no bases deposited for entire structure), and 6sg9 (some residues with bases, others without).  Using: DSSR v1.9.10-2020apr23.

Thanks,

Cathy

Title: Re: DSSR eta-base theta-base
Post by: xiangjun on January 09, 2021, 07:19:44 pm

Hi Cathy,

Happy 2021!

Following your request, I've updated DSSR so that the JSON output for pseudo-torsion angles eta_base and theta_base would be "null" instead of 0.0 when they cannot be calculated. I have also refined DSSR to account for chain breaks while calculating all pseudo torsions.

The updated DSSR (v2.2.1) will be available from the Columbia Technology Ventures (CTV) website (http://innovation.columbia.edu/technologies/CU20391), presumably by early next week. As you may know, DSSR is now licensed by Columbia University.

Best regards,

Xiang-Jun

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.