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The issue on proper ordering of multiple chains to avoid crossing lines (false pseudoknots) has been formally addressed by Dirks et al. in their 2007 article titled Thermodynamic analysis of interacting nucleic acid strands (SIAM Rev, 49, 65-88), specifically in Section 2.1 (Fig. 2.1). Applying that algorithm to nucleic acid structures, however, is beyond the scope of DSSR. The program strictly respects the ordering of chains and nucleotides within a given PDB or PDBx/mmCIF file, but outputs warning messages where necessary to draw users’ attention. As another example, I’ve recently noticed that DNA duplexes produced by Maestro (a product of Schrödinger) list nucleotides of the complementary strand in 3′ to 5′ order to match the 5′ to 3′ directionality of the leading strand for each Watson-Crick pair (See below).
File name: 1h1k.pdb
no. of DNA/RNA chains: 6 [I=412,J=276,K=265,L=412,M=276,N=265]
no. of nucleotides: 1906
no. of atoms: 40008
no. of waters: 0
no. of metals: 0
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Special notes:
o cross-paired segments in separate chains, be *careful* with .dbn
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This structure contains *2-order pseudoknot
o You may want to run DSSR again with the '--nested' option which removes
pseudoknots to get a fully nested secondary structure representation.
o The DSSR-derived dbn may be problematic (see notes above).
When specifying --nest, is this equivalent to replacing all {}, <>, etc. with "." in the DBN?
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.