Example:
$ rna_pdb_tools.py --fetch 1xjr downloading...1xjr ok
Example:
$ rna_pdb_tools.py --fetch_ba 1xjr downloading...1xjr_ba.pdb ok
or over a list of pdb ids in a text file:
$ cat data/pdb_ids.txt 1y26 1fir $ while read p; do rna_pdb_tools.py --fetch_ba $p; done < data/pdb_ids.txt downloading...1y26_ba.pdb ok downloading...1fir_ba.pdb ok $ ls *.pdb 1fir_ba.pdb 1y26_ba.pdb
Example:
[mm] original$ for i in `ls *.pdb`; do rna_pdb_tools.py --get_seq $i; echo ''; done > 10_BUJNICKI_1 A:1-75 GCGGAAGUAGUUCAGUGGUAGAACACCACCUUGCCAAGGUGGGGGUCGCGGGUUCGAAUCCCGUCUUCCGCUCCA > 10_BUJNICKI_1 B:1-96 UGCGAUGAGAAGAAGAGUAUUAAGGAUUUACUAUGAUUAGCGACUCUAGGAUAGUGAAAGCUAGAGGAUAGUAACCUUAAGAAGGCACUUCGAGCA > 10_BUJNICKI_10 A:1-75 GCGGAAGUAGUUCAGUGGUAGAACACCACCUUGCCAAGGUGGGGGUCGCGGGUUCGAAUCCCGUCUUCCGCUCCA > 10_BUJNICKI_10 B:1-96 UGCGAUGAGAAGAAGAGUAUUAAGGAUUUACUAUGAUUAGCGACUCUAGGAUAGUGAAAGCUAGAGGAUAGUAACCUUAAGAAGGCACUUCGAGCA > 10_BUJNICKI_2 A:1-75 GCGGAAGUAGUUCAGUGGUAGAACACCACCUUGCCAAGGUGGGGGUCGCGGGUUCGAAUCCCGUCUUCCGCUCCA > 10_BUJNICKI_2 B:1-96 UGCGAUGAGAAGAAGAGUAUUAAGGAUUUACUAUGAUUAGCGACUCUAGGAUAGUGAAAGCUAGAGGAUAGUAACCUUAAGAAGGCACUUCGAGCA > 10_BUJNICKI_3 A:1-75 GCGGAAGUAGUUCAGUGGUAGAACACCACCUUGCCAAGGUGGGGGUCGCGGGUUCGAAUCCCGUCUUCCGCUCCA > 10_BUJNICKI_3 B:1-96 UGCGAUGAGAAGAAGAGUAUUAAGGAUUUACUAUGAUUAGCGACUCUAGGAUAGUGAAAGCUAGAGGAUAGUAACCUUAAGAAGGCACUUCGAGCA > 10_BUJNICKI_4 A:1-75 GCGGAAGUAGUUCAGUGGUAGAACACCACCUUGCCAAGGUGGGGGUCGCGGGUUCGAAUCCCGUCUUCCGCUCCA > 10_BUJNICKI_4 B:1-96 UGCGAUGAGAAGAAGAGUAUUAAGGAUUUACUAUGAUUAGCGACUCUAGGAUAGUGAAAGCUAGAGGAUAGUAACCUUAAGAAGGCACUUCGAGCA
Examples:
$ for i in `ls *pdb`; do rna_pdb_tools.py --delete A:46-56 $i > ../rpr_rm_loop/$i ; done
go over all files in the current directory, remove a fragment of chain A, residues between 46-56 (including them) and save outputs to in the folder rpr_rm_loops.
Rename chain B in structure 4_das_1_rpr.pdb:
$ rna_pdb_tools.py --get_seq 4_das_1_rpr.pdb > 4_das_1_rpr.pdb B:1-126 GGCUUAUCAAGAGAGGUGGAGGGACUGGCCCGAUGAAACCCGGCAACCACUAGUCUAGCGUCAGCUUCGGCUGACGCUAGGCUAGUGGUGCCAAUUCCUGCAGCGGAAACGUUGAAAGAUGAGCCA $ rna_pdb_tools.py --edit 'B:1-126>A:1-126' 4_das_1_rpr.pdb > 4_das_1_rpr2.pdb $ rna_pdb_tools.py --get_seq 4_das_1_rpr2.pdb > 4_das_1_rpr2.pdb A:1-126 GGCUUAUCAAGAGAGGUGGAGGGACUGGCCCGAUGAAACCCGGCAACCACUAGUCUAGCGUCAGCUUCGGCUGACGCUAGGCUAGUGGUGCCAAUUCCUGCAGCGGAAACGUUGAAAGAUGAGCCA
Examples:
$ rna_pdb_tools.py --edit 'A:3-21>A:1-19' 1f27_clean.pdb > 1f27_clean_A1-19.pdb
or even:
$ rna_pdb_tools.py --edit 'A:3-21>A:1-19,B:22-32>B:20-30' 1f27_clean.pdb > 1f27_clean_renumb.pdb
or even, even, do rename X chain to A only for Chen's pdb structures in the folder, in place (so don't create a new file):
for i in `ls *Chen*`; do rna_pdb_tools.py --edit 'X:1-125>A:1-125' $i > ${i}_temp; mv ${i}_temp ${i}; done # do only edit for Chen's pdb structures, in place.
Run:
$ rna_pdb_tools.py --get_rnapuzzle_ready input/1_das_1_rpr_fixed.pdb HEADER Generated with rna-pdb-tools HEADER ver 91ed4f8-dirty HEADER https://github.com/mmagnus/rna-pdb-tools HEADER Sun Mar 5 10:58:07 2017 REMARK 000 Missing atoms: REMARK 000 + P B <Residue C het= resseq=1 icode= > residue # 1 REMARK 000 + OP1 B <Residue C het= resseq=1 icode= > residue # 1 REMARK 000 + OP2 B <Residue C het= resseq=1 icode= > residue # 1 REMARK 000 + O5' B <Residue C het= resseq=1 icode= > residue # 1 ATOM 1 P C A 1 -16.936 -3.789 68.770 1.00 11.89 P ATOM 2 OP1 C A 1 -17.105 -3.675 67.302 1.00 14.35 O ATOM 3 OP2 C A 1 -15.666 -4.265 69.342 1.00 12.68 O ...
.. argparse:: :ref: rna_pdb_tools.rna_pdb_rnapuzzle_ready.get_parser :prog: rna_pdb_rnapuzzle_ready.py
The tool is using the function:
.. automethod:: rna_pdb_tools.pdb_parser_lib.StrucFile.get_rnapuzzle_ready