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RNA structures (DSSR) / discarded nucleotides in json output
« on: March 04, 2018, 08:36:01 am »

First, many thanks for your great software suite. It is a real pleasure to work with such complete and convenient outputs for my parsing purposes. I am a strong believer in collaboration in methods development trough connectible building blocs, and it is nice to have others with such view in the RNA-modeling field  :)

I am building specific structural fragment libraries for RNA docking, and I try to parse dssr json outputs to automatically keep track of my fragments characteristics (2D structure, interactions ...). For this, I need to now which nucleotides were discarded because of e.g. weird geometry. As I see it, a "&" is inserted in the "bseq" entry for chain breaks. But I can't find any indication of if a nucleotide was discarded or the break was already present in the input pdb, and retrieving it by comparing bseq to the input sequence can be ambiguous.
I am considering using the "Summary of structural features of xx nucleotides" in the text output, by running dssr w. and wo. the "--json" option. Is there a dssp option I could use to get the info directly from the json output and avoid double work (as I am analysing thousands of pdb files)?

Thanks in advance for your help,
Isaure C. de Beauchene

PS: I'm using version v1.7.2-2017nov20

RNA structures (DSSR) / brackets in DNA-RNA pairing
« on: January 15, 2018, 10:19:45 am »

I ran dssr locally on PDB 4OO8, which contains 2 symmetrical copies of a RNA-DNA duplex, made of chains E-F and B-C. The only difference in the 2 duplexes is 3 additional bases in 5' of the DNA chain.
However, the secondary structure given for each duplex is different:

for DNA - RNA:
chain_C['sstr'], chain_B['sstr'] =  '[[[[[[[[[[[[[[[[[[[[',  ']]]]]]]]]]]]]]]]]]]]'
chain_F['sstr'], chain_E['sstr'] = '((((((((((((((((((((' , '))))))))))))))))))))'

When running dssr on, the secondary structure is identical for the 2 duplexes (with round brackets).
So what is the meaning of the squared brackets in the local version?

Thanks in advance,

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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.