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Get RNA only chains based on sequences in a PDB file

Marcin Magnus edited this page May 15, 2019 · 1 revision
[mm] z_ISL$ rna_pdb_toolsx.py --get_seq 5y88.pdb
# 5y88
> A:127-431 450-1576 1603-1827 1840-2085 3000-3000
(...)
> D:1-101
GUUCGCGAAGUAACCCUUCGUGGACAUUUGGUCAAUUUGAAACAAUACAGAGAUGAUCAGCAGUUCCCCUGCAUAAGGAUGAACCGUUUUACAAAGAGAUU
> E:1-15 492-504
GUAUGUAUUUAUUUUUAGAUACUAACAC
> F:1-43 110-123 1096-1120
ACGAAUCUCUUUGCCUUUUGGCUUAGAUCAAGUGUAGUAUCUGACAUUUUUUGGCACCGCGACCCUCGCACUUGUGGAGUCG
> G:1-8 12-32 50-175
tpyurelpeopyrsnuepnulssueanesapnrlrrurnaurrurusngnnssggropenpppprueuuurggsrogeprrgreonurrulruuyelprrussnuelupruuonrlrnnpgennpregnrsreluutnenngsnenpuuergsgu
(...)
> t:1-53 57-65 77-139
tusaerysloggolurosrgreeusruuunrlsprynpoernuoureuuelueannarurureonuurrunnuppaetuunesugrruprurssurrltrugpaasulaanuutusnuprspuos
> x:1-9
UUUUUUUUU
[mm] z_ISL$ rna_pdb_toolsx.py --get-chain BDEFx 5y88.pdb > 5y88_RNAOnly.pdb
[mm] z_ISL$ rna_pdb_toolsx.py --get_seq 5y88_RNAOnly.pdb
# 5y88_RNAOnly
> B:28-55 60-127 163-183
GGAGGUCAACAUCAAGAACUGUGGGCCUUUGCCUAUAGAACUUAUAACGAACAUGGUUCUUGCCUUUUACCAGAACCAUCCGGGUGUUGUCUCCAUCCAUAUUUUUUGGAACUUUUC
> D:1-101
GUUCGCGAAGUAACCCUUCGUGGACAUUUGGUCAAUUUGAAACAAUACAGAGAUGAUCAGCAGUUCCCCUGCAUAAGGAUGAACCGUUUUACAAAGAGAUU
> E:1-15 492-504
GUAUGUAUUUAUUUUUAGAUACUAACAC
> F:1-43 110-123 1096-1120
ACGAAUCUCUUUGCCUUUUGGCUUAGAUCAAGUGUAGUAUCUGACAUUUUUUGGCACCGCGACCCUCGCACUUGUGGAGUCG
> x:1-9
UUUUUUUUU