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 | ||
==External links== | ==External links== | ||
Revision as of 06:37, 25 April 2007
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
