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Author Topic: DSSR eta-base theta-base  (Read 74 times)

Offline cllawson

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DSSR eta-base theta-base
« 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

Offline xiangjun

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Re: DSSR eta-base theta-base
« Reply #1 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, presumably by early next week. As you may know, DSSR is now licensed by Columbia University.

Best regards,

Xiang-Jun


« Last Edit: January 10, 2021, 07:47:07 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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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.