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« 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:
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