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Author Topic: strange sequence and dot-bracket notation for dssr output  (Read 112 times)

Offline shuxiang

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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

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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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline shuxiang

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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

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.