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1 <tool id="PDBTIDY" name="PDBTIDY" version="1">
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2 <description>Using pdb_tidy tools after ab_haddock_format.py.</description>
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3 <command detect_errors="exit_code"><![CDATA[
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4 source /home/galaxy/data/_conda/bin/activate pdbtools;
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5 pdb_tidy '${input}' > '${output}';
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6 source /home/galaxy/data/_conda/bin/deactivate
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7 ]]></command>
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8 <inputs>
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9 <param name="input" format="pdb" type="data" label="Select your PDB file."/>
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10 </inputs>
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11 <outputs>
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12 <data name="output" format="pdb" />
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13 </outputs>
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14 <help>
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15 Modifies the file to adhere (as much as possible) to the format specifications.
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16 Expects a sorted file - REMARK/ATOM/HETATM/END - so use pdb_sort in case you are
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17 not sure.
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18
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19 This includes:
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20 - Adding TER statements after chain breaks/changes
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21 - Truncating/Padding all lines to 80 characters
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22 - Adds END statement at the end of the file
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23
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24 Will remove all original TER/END statements from the file.
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25
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26 Usage:
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27 python pdb_tidy.py 'pdb file'
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28
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29 Example:
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30 python pdb_tidy.py 1CTF.pdb
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31
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32 This program is part of the 'pdb-tools' suite of utilities and should not be
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33 distributed isolatedly. The 'pdb-tools' were created to quickly manipulate PDB
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34 files using the terminal, and can be used sequentially, with one tool streaming
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35 data to another. They are based on old FORTRAN77 code that was taking too much
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36 effort to maintain and compile. RIP.
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37 </help>
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38 </tool>
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39
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