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

Author Topic: strange sequence and dot-bracket notation for dssr output  (Read 18651 times)

Offline shuxiang

  • with-posts
  • *
  • Posts: 56
    • View Profile
strange sequence and dot-bracket notation for dssr output
« on: June 21, 2019, 02:32:10 pm »
Hi Xiang-Jun,

We just came across a strange sequence and dot-bracket notation for the dssr output.
open http://dssr.x3dna.org/ , type in 4v91, go the Secondary structures in dot-bracket notation section. You will see something as following:

>4v91 nts=3482 [whole]
U&U&GACCUCA&AA&UCAGGUAGGAGUACCCG&CUGA&AC&UUAAGCAU&AUCAAUAAGCG&G

A lot of "&"s  are inserted in sequence and dot-bracket notation. It looks like a bug for the output.

Best,
Shuxiang

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1650
    • View Profile
    • 3DNA homepage
Re: strange sequence and dot-bracket notation for dssr output
« Reply #1 on: June 21, 2019, 03:21:43 pm »
Hi Shuxiang,

Quote
A lot of "&"s  are inserted in sequence and dot-bracket notation. It looks like a bug for the output.

It is not a bug, but a feature in DSSR. Read "3.18.12 The --dbn-break option" in the DSSR manual.

For this special case, the atomic model is in bad geometry (even though it has a nominal resolution of 3.7 Å). See the attached image for nucleotides 1-3 (GGU) of chain 3. This is sort of like the 3DNA-rebuilt models with an approximate backbone conformation that needs to be optimized (using Phenix as shown in our web 3DNA 2.0 paper).

You could use "--dbn-break=no" to remove the & symbols, as documented in the DSSR manual.

Best regards,

Xiang-Jun

Offline shuxiang

  • with-posts
  • *
  • Posts: 56
    • View Profile
Re: strange sequence and dot-bracket notation for dssr output
« Reply #2 on: June 21, 2019, 03:31:57 pm »
Hi, Xiang-Jun,

Thank you for your reply. I already added this option for the command-line based analysis.

Best :),
Shuxiang

 

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