Difference between revisions of "Pdbset (ccp4)"
From Christoph's Personal Wiki
(→Example usage) |
|||
| (One intermediate revision by the same user not shown) | |||
| Line 1: | Line 1: | ||
'''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
