Messages

1

RNA structures (DSSR) / Re: DSSR output - Base pair characteristics

« on: March 26, 2013, 01:56:53 pm »

Thank you for the prompt response. This cleared things up!

FYI, I had a typo in my original post. The basepairs were extracted from PDBID: 3OX0 [http://www.rcsb.org/pdb/explore.do?structureId=3OX0] (got my O's and 0's confused)

Jose

2

RNA structures (DSSR) / DSSR output - Base pair characteristics

« on: March 26, 2013, 11:19:15 am »

Hi all,

Loving DSSR for analyzing RNA structures! I was wondering what are all the qualitative parameters about base pairs that are captured by this tool are. For example I ran DSSR on PDBID 3OXO the and following (abridged) sample base pair details are given:

Code: [Select]

3 A.C3             A.G86            [C-G] WC           19-XIX    cWW cW-W
...
8 A.G7             B.A64            [G+A] Linker       00-n/a    tSS tm+m
...
9 A.G8             A.A81            [G-A]              00-n/a    tSH tm-M
...
22 A.G32            A.A71            [G+A]              00-n/a    cH. cM+.


Where for the case of base pair #3, I have recognized the following annotations:
- "3": Base pair number
- "A.C3": Chain 1, residue identifier 1, residue position 1
- "A.G86": Chain 2, residue identifier 2, residue position 2
- "[C-G] WC": A descriptive label for this base pair
- "19-XIX": The Saenger class for this base pair (00-n/a when not available)
- "cWW": The Leontis-Westhof nomenclature for interacting edges (cis Watson-Crick/Watson-Crick -> Class #1)

However what does the last column refer to? For example:
Base pair #3: "cW-W"
Base pair #8: "tm+m"
Base pair #9: "tm-M"
Base pair #22: "cM+."

Also, what does the "." signify when found in either of the last two columns of this output?

Regards,
Jose