I'm trying to find a programmatic way to automatically extract the following information from a PDB file:RNA sequence Secondary structure restraints in bracket format, e.g. . (( . ( . ) . ))Does software exist that can take a PDB file as input and generate these two pieces of information? e.g. file. 3NDB_ba.pdbThe nucleotide sequence is: gUCUCGUCCCGUGGGGCUCGGCGGUGGGGGAGCAUCUCCUGUAGGGGAGAUGUAACCCCCUUUACCUGCCGAACCCCGCCAGGCCCGGAAGGGAGCAACGGUAGGCAGGACGUCGGCGCUCACGGGGGUGCGGGAC.And the secondary structure :.(((.(..(((((((((.(((((..(((((.(((((((((....)))))))))..)))))....((((((.....(((.....(((....))).....)))..)))))).))))))).))))))).....).))).
How to extract RNA sequence and secondary structure restrains from a PDB file
public databases;pdb;rna;rna structure
I suggest you take a look at rna-pdb-tools we do way more than you need! :-) The tools can get you a sequence, secondary structure and much more using various algorithms, and all is well documented http://rna-pdb-tools.readthedocs.io/en/latest/To get sequence http://rna-pdb-tools.readthedocs.io/en/latest/main.html#get-sequence $ rna_pdb_tools.py --get_seq 5_solution_1.pdb> 5_solution_1.pdb A:1-576CAUCCGGUAUCCCAAGACAAUCUCGGGUUGGGUUGGGAAGUAUCAUGGCUAAUCACCAUGAUGCAAUCGGGUUGAACACUUAAUUGGGUUAAAACGGUGGGGGACGAUCCCGUAACAUCCGUCCUAACGGCGACAGACUGCACGGCCCUGCCUCAGGUGUGUCCAAUGAACAGUCGUUCCGAAAGGAAGor you can get sequence and secondary structure via x3dna (http://x3dna.org/)[mm] py3dna$ git:(master)  ./rna_x3dna.py test_data/1xjr.pdbtest_data/1xjr.pdb >1xjr nts=47 [1xjr] -- secondary structure derived by DSSR gGAGUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUU ..(((((((...((((.((((.....))..))..))).).)))))))The problem is not trivial. I hope rna-pdb-tools has stuff that can solve this issue for you (http://rna-pdb-tools.readthedocs.io/en/latest/want.html#module-rna_pdb_tools.utils.rna_x3dna.rna_x3dna)