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PDBj (Protein Data Bank Japan) maintains a centralized archive of macromolecular structures and provides integrated tools, in collaboration with the RCSB, the BMRB in USA and the PDBe in EU. PDBj is supported by JST-BIRD.
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Sample programs to handle PDBML |
| Archive name |
Description |
Files included |
Requirement |
| filter.tar.gz |
Select specified elements
(and those below them) |
pdbML-filter.pl...perl script
filter.txt...a text file to specify elements/tags
readme.txt...documentation
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perl ver.5.005 or later
XML::Parser perl module
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| filter2.tar.gz |
Delete elements and/or rename tags |
pdbML-filter2.pl...perl script
del_rename.txt...a text file to specify elements/tags
readme.txt...documentation
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perl ver.5.005 or later
XML::DOM perl module
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| addtag.tar.gz |
Add new elements |
addtag.pl...perl script
tag_define.xml...an XML file with the new elements
readme.txt...document
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perl ver.5.005 or later
XML::DOM perl module
XML::XQL perl module
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| parse_extatom.tar.gz |
parse extatom file |
parse_extatom.pl...perl script
readme.txt...document
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perl ver.5.005 or later
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