Difference between revisions of "Pdbset (ccp4)"
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'''pdbset''' — is part of the [[:Category:ccp4|ccp4]] package and has various useful manipulations on coordinate files (e.g., [[PDB]] files). | '''pdbset''' — is part of the [[:Category:ccp4|ccp4]] package and has various useful manipulations on coordinate files (e.g., [[PDB]] files). | ||
− | ==Syntax | + | ==Syntax== |
pdbset XYZIN foo_in.pdb XYZOUT foo_out.pdb | pdbset XYZIN foo_in.pdb XYZOUT foo_out.pdb | ||
[Keyworded input] | [Keyworded input] | ||
− | ==Keyworded input | + | ==Keyworded input== |
*The available keywords are: | *The available keywords are: | ||
<code>BFACTOR, CELL, CHAIN, COM, ELEMENT, EXCLUDE, OCCUPANCY, ORTHOGONALIZATION, OUTPUT, PICK, REMARK, RENUMBER, REORTHOGONALIZE, REPLACE, ROTATE, SELECT, SEQUENCE, SHIFT, SPACEGROUP, SYMGEN, TRANSFORM, UTOB, XPLOR, NOISE, ATRENUMBER</code> | <code>BFACTOR, CELL, CHAIN, COM, ELEMENT, EXCLUDE, OCCUPANCY, ORTHOGONALIZATION, OUTPUT, PICK, REMARK, RENUMBER, REORTHOGONALIZE, REPLACE, ROTATE, SELECT, SEQUENCE, SHIFT, SPACEGROUP, SYMGEN, TRANSFORM, UTOB, XPLOR, NOISE, ATRENUMBER</code> | ||
==Example usage== | ==Example usage== | ||
− | #!/bin/sh -f | + | #!/bin/sh -f |
− | pdbset xyzin input.pdb xyzout output.pdb << eof | + | pdbset xyzin input.pdb xyzout output.pdb << eof |
− | OCCUPANCY RESET 90 | + | OCCUPANCY RESET 90 |
− | BFACTOR ALWAYS 0 | + | BFACTOR ALWAYS 0 |
− | eof | + | eof |
+ | Or, | ||
+ | echo "BFACTOR ALWAYS 0" | pdbset xyzin input.pdb xyzout output.pdb | ||
+ | |||
+ | ===Extended examples=== | ||
+ | ''Note: These were taken directly from the man page.'' | ||
+ | <pre> | ||
+ | ######################## Convert PDB file to mmCIF format | ||
+ | #!/bin/csh -f | ||
+ | # | ||
+ | pdbset xyzin toxd.pdb xyzout toxd.cif << eof-1 | ||
+ | output cif | ||
+ | end | ||
+ | eof-1 | ||
+ | |||
+ | ######################## Take output from O into a form suitable for refinement | ||
+ | #!/bin/csh -f | ||
+ | # | ||
+ | pdbset xyzin bst_113m.pdb xyzout temp1.pdb << eof-1 | ||
+ | cell 132.02 115.21 96.20 90.00 90.00 90.00 | ||
+ | spacegroup P212121 | ||
+ | eof-1 | ||
+ | |||
+ | ################### Take output from Xplor into a form suitable for refinement | ||
+ | #!/bin/csh -f | ||
+ | # | ||
+ | pdbset xyzin bst_113m.pdb xyzout temp1.pdb << eof-1 | ||
+ | cell 132.02 115.21 96.20 90.00 90.00 90.00 | ||
+ | spacegroup P212121 | ||
+ | xplor | ||
+ | eof-1 | ||
+ | |||
+ | |||
+ | |||
+ | ######################## Expand dimer to tetramer, rename chains, transform | ||
+ | #!/bin/csh -f | ||
+ | # | ||
+ | # Make tetramer from dimer | ||
+ | # | ||
+ | pdbset xyzin ecrproducts268.pdb xyzout ecrprodpqrtet.pdb <<eof-1 | ||
+ | remark Tetramer generated from AB dimer | ||
+ | remark rotated to pqr frame | ||
+ | remark | ||
+ | ! Generate other dimer by z-dyad in P21212 | ||
+ | symgen x,y,z | ||
+ | symgen -x,-y,z | ||
+ | ! Rename chains in second dimer: V & W are water chains | ||
+ | chain symmetry 2 A C | ||
+ | chain symmetry 2 B D | ||
+ | chain symmetry 2 V X | ||
+ | chain symmetry 2 W Y | ||
+ | ! transform to molecular frame | ||
+ | transform - | ||
+ | 0.87831 0.47808 0 - | ||
+ | 0 0 -1. - | ||
+ | -0.47808 0.87831 0 - | ||
+ | 0.0 -2.713 0.0 | ||
+ | eof-1 | ||
+ | </pre> | ||
==External links== | ==External links== |
Latest revision as of 01:34, 9 July 2012
pdbset — is part of the ccp4 package and has various useful manipulations on coordinate files (e.g., PDB files).
Syntax
pdbset XYZIN foo_in.pdb XYZOUT foo_out.pdb [Keyworded input]
Keyworded input
- The available keywords are:
BFACTOR, CELL, CHAIN, COM, ELEMENT, EXCLUDE, OCCUPANCY, ORTHOGONALIZATION, OUTPUT, PICK, REMARK, RENUMBER, REORTHOGONALIZE, REPLACE, ROTATE, SELECT, SEQUENCE, SHIFT, SPACEGROUP, SYMGEN, TRANSFORM, UTOB, XPLOR, NOISE, ATRENUMBER
Example usage
#!/bin/sh -f pdbset xyzin input.pdb xyzout output.pdb << eof OCCUPANCY RESET 90 BFACTOR ALWAYS 0 eof
Or,
echo "BFACTOR ALWAYS 0" | pdbset xyzin input.pdb xyzout output.pdb
Extended examples
Note: These were taken directly from the man page.
######################## Convert PDB file to mmCIF format #!/bin/csh -f # pdbset xyzin toxd.pdb xyzout toxd.cif << eof-1 output cif end eof-1 ######################## Take output from O into a form suitable for refinement #!/bin/csh -f # pdbset xyzin bst_113m.pdb xyzout temp1.pdb << eof-1 cell 132.02 115.21 96.20 90.00 90.00 90.00 spacegroup P212121 eof-1 ################### Take output from Xplor into a form suitable for refinement #!/bin/csh -f # pdbset xyzin bst_113m.pdb xyzout temp1.pdb << eof-1 cell 132.02 115.21 96.20 90.00 90.00 90.00 spacegroup P212121 xplor eof-1 ######################## Expand dimer to tetramer, rename chains, transform #!/bin/csh -f # # Make tetramer from dimer # pdbset xyzin ecrproducts268.pdb xyzout ecrprodpqrtet.pdb <<eof-1 remark Tetramer generated from AB dimer remark rotated to pqr frame remark ! Generate other dimer by z-dyad in P21212 symgen x,y,z symgen -x,-y,z ! Rename chains in second dimer: V & W are water chains chain symmetry 2 A C chain symmetry 2 B D chain symmetry 2 V X chain symmetry 2 W Y ! transform to molecular frame transform - 0.87831 0.47808 0 - 0 0 -1. - -0.47808 0.87831 0 - 0.0 -2.713 0.0 eof-1