Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Questions and answers > RNA structures (DSSR)

Groove width distance in DSSR

(1/4) > >>

lvelve0901:
Hi, xiangjun,

Did DSSR output json files have minor groove width information?

If so, could you kindly tell me where is it stored in the json file?

Best,
Honglue

xiangjun:
Hi Honglue,

The groove dimensions as in the 3DNA/analyze program are currently not calculated in DSSR. So no minor-groove width info in the JSON output, as of DSSR v1.6.5-2017jan22.

It's not hard to add the groove info in the DSSR JSON output. Do you have any preference as to how to present it in JSON?

From 3DNA/analyze, an example output for 355d is as below:


--- Code: ---                  Minor Groove        Major Groove
                 P-P     Refined     P-P     Refined
   1 CG/CG       ---       ---       ---       ---
   2 GC/GC       ---       ---       ---       ---
   3 CG/CG      14.3       ---      18.2       ---
   4 GA/TC      12.0      11.9      17.3      17.3
   5 AA/TT       9.7       9.6      19.1      19.0
   6 AT/AT       9.1       9.1      16.4      16.0
   7 TT/AA       9.1       9.1      17.8      17.7
   8 TC/GA       9.6       9.6      18.6      18.6
   9 CG/CG      10.4       ---      19.0       ---
  10 GC/GC       ---       ---       ---       ---
  11 CG/CG       ---       ---       ---       ---

--- End code ---

The whole section could be listed as an array of strings. Or each of the four columns can be indexed separately.

What's your thought?

Xiang-Jun

lvelve0901:
Hi, xiangjun,

Thank you so much!

Since minor groove width are dinucleotide step in 3DNA, how about we incorporate them into the 'pairs' in the 'helices' where the step and helical parameters stored?

What do you think?

Best,
Honglue

xiangjun:
That makes sense. I'll implement this feature by next week (I'm facing a deadline for a ms submission).

I'll keep you informed once a preliminary version is available for you check. Stay tuned.

Xiang-Jun

lvelve0901:
Hi, Xiangjun,

Any update about incorporate groove width in json file?

Here is the an example of the structure I want to calculate and its old output json file using "x3dna-dssr -i=A2dna.pdb -o=A2dna.json --json --more". Hope this will be helpful.

Thank you again for your time.

Best,
Honglue

Navigation

[0] Message Index

[#] Next page

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.