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Questions and answers > RNA structures (DSSR)

Groove width distance in DSSR

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xiangjun:
Hi Honglue,

Thanks for sending me the two files. I did not forget your request, and I am hoping to get it done in a couple of days...

Xiang-Jun

xiangjun:
Hi Honglue,

Just to let you know that I've been working on the feature (groove info to DSSR) you requested. While at it, I'm considering to include other related features from the 3DNA analyze program to DSSR, presumably only via the JSON output.

In addition to groove widths, are there other 3DNA features you'd like to see in DSSR JSON output?

Best regards,

Xiang-Jun

lvelve0901:
Hi, xiangjun,

I just want to let you know I really appreciate your help!

For other parameters, I need to think about it and get it back to you. Could you kindly remind me any parameter not included in DSSR but in 3DNA? Did the DSSR manual have something about these "missing" parameters?

I will probably response to you either Saturday or Sunday.

Best,
Honglue

xiangjun:
Hi Honglue,

I always value users' feedback, like yours.

Have a look of the output from the following command, and check file "355d.out":


--- Code: ---find_pair 355d.pdb | analyze --abi
--- End code ---

I'd add the A/B-index, maybe Zp as well... You'll be able to have access to a test version by early next week (no later than Tuesday, I hope).

Have a good weekend.

Xiang-Jun

xiangjun:
Hi Honglue,

I've finally added groove widths into DSSR JSON output, per your request. Now with --more, you will see the groove_widths key in helices/stems output. The corresponding value is an array with 4 numbers: [minor_groove_width, major_groove_width, minor_groove_width_refined, major_groove_width_refined], as they appear in the 3DNA analyze output. For example, "groove_widths":[12.023,11.942,17.338,17.281] for the 4th dinucleotide step in 355d.

As mentioned in my previous responses, some additional features from the 3DNA analyze program have been implemented into DSSR. They will be revealed later.

Please have try and report back how it goes. Note I've not updated the release version on the download page yet. However, the download files have been updated.

Best regards,

Xiang-Jun

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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.