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Hi,
I cannot reproduce your reported result based on information provided (i.e., PDB id: 4gma). Could you please be more specific by attached the PDB file, DSSR version, and options you used?
Thanks,
Xiang-Jun
In DSSR, a loop forms a ‘closed’ circle with any two sequential nucleotides connected either by a phosphodiester linkage or a canonical base pair, and is specified by the lengths of consecutive bridging-nucleotide segments (Figures 1F and 2C).
OK. I got it. I'll look into the issue.
Regarding the definition of (junction) loops, the DSSR paper says:QuoteIn DSSR, a loop forms a ‘closed’ circle with any two sequential nucleotides connected either by a phosphodiester linkage or a canonical base pair, and is specified by the lengths of consecutive bridging-nucleotide segments (Figures 1F and 2C).
The situation becomes less intuitive/obvious when pseudoknots are included. You could try the --nested option to removed pseudoknots to see if the results make more sense.
Best regards,
Xiang-Jun
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.