PDBSET (CCP4: Supported Program)
pdbset - various useful manipulations on coordinate files
pdbset XYZIN foo_in.pdb XYZOUT foo_out.pdb
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
In the description below, optional items are in , alternatives are separated by |, keywords are in uppercase, parameters (i.e. numbers) are in lowercase. The input itself is case-insensitive for keywords (but parameters e.g. chain IDs must of course be the correct case). In the output file, the chain ID is always uppercase.
CELL a b c [alpha beta gamma]
Read cell dimensions and make CRYST1 & SCALE header records. These will replace any CRYST1 & SCALE lines already present in file. The CRYST1 line should have the spacegroup in it, so a SPACEGROUP command is recommended.
ORTHOGONALIZATION (or NCODE) orthogonalization_code
Define code to generate orthogonalization matrix from input cell. This is not normally required, and only has an effect if a CELL command is also given.
Code :- = 1 axes along a, c* x a, c* (Brookhaven standard, default) = 2 axes along b, a* x b, a* = 3 axes along c, b* x c, b* = 4 axes along a+b, c* x (a+b), c* = 5 axes along a*, c x a*, c ( Rollett ) = 6 axes along a, b*, a x b* = 7 axes along a*, b, a* x b (TNT convention, probably not very useful here since TNT has its own converter program)
Read spacegroup name (not essential, but put into CRYST1 line on output)
SYMGEN Spacegroup_name | Spacegroup_number | Symmetry_operation | NCS
Generate chains with these symmetry operations applied. If the operations are given explicitly, several SYMGEN commands may be given. The identity operation must be specified explicitly if required. Use the CHAIN command to rename them. Note that, except for NCS, these symmetry operations apply to fractional coordinates, so the orthogonalization operation must be known to the program, either from CRYST1 and/or CELL lines in the input coordinate file, or from a CELL command. If the keyword NCS is given, then a series of TRANSFORM commands should be given to define the non-crystallographic symmetry operations to be used.
NB: if supplying individual symmetry operations, these must be in the form found in the file symop.lib, e.g.
SYMGEN -X,Y,-Z SYMGEN 1/2+X,1/2+Y,ZElements within each operation are separated by commas. To supply multiple operations on a single line, separate each pair of operations by an asterisk, e.g.
SYMGEN -X,Y,-Z * 1/2+X,1/2+Y,Z
RENUMBER [INCREMENT] start|increment [residue range] [CHAIN old_chain [TO new_chain]]
Renumber or add constant to residue numbers in given range. The residue
range is given as 1st_residue_number [TO] last_residue_number. If the CHAIN
keyword is present, the renumbering applies only to this chain. The option
TO new_chain causes the chain identifier to be changed. Note that renumbering
is done after chain renaming specified by the CHAIN command, so the chain
specified here (old_chain) is the chain ID after any renaming. N.B. there
is NO check that different RENUMBER commands are mutually exclusive. To
avoid problems with recursive renumbering, if more than one RENUMBER command
would apply to a residue, only the first will be done.
e.g. RENUMBER 35 ! renumber all residues, starting from 35 RENUMBER INCREMENT -5 102 TO 110 CHAIN C ! subtract 5 from ! residues 102 to 110 in chain C RENUMBER 101 1 TO 78 CHAIN A TO B ! renumber residues 1 to 78 in chain A from 101 (to 178), ! changing the chain identifier to B
CHAIN [SYMMETRY Nsym] [old_chain] new_chain
Change chain ID to given value. If only one value given, change all chains to this value. If SYMMETRY keyword given, this applies to this symmetry operation only. A series of CHAIN commands may be given.
e.g. CHAIN Q ! change all chains to Q CHAIN SYMMETRY 2 A B ! change chain generated from chain A ! by symmetry operation 2 to B
BFACTOR [subkey] B_reset (B_reset2)
Set B-factor (default 20.0).
OCCUPANCY [subkey] Occ_reset (Occ_reset2)
Set occupancy (default 1.0).
ROTATE [INVERT] [MATRIX|EULER|POLAR] values
Define rotational transformation, either as MATRIX (this keyword may be omitted) followed by 9 numbers (r11 r12 r13 r21 r22 r23 r31 r32 r33), by keyword EULER followed by Eulerian angles alpha, beta, gamma (as in ALMN), or by keyword POLAR followed by polar angles omega, phi, kappa (as in POLARRFN). This transformation will be applied to all atoms. The SHIFT command may be used to define a translation in addition. The transformation defined by ROTATE & SHIFT, or by TRANSFORM, is applied after any SYMGEN operation. Multiple definitions of ROTATE or TRANSFORM, or of SHIFT will NOT be concatenated: only the last will be effective.
The subkey INVERT causes the inverse transformation to be applied. Note that an INVERT instruction if present will apply to both ROTATE & SHIFT.
SHIFT [INVERT] [FRACTIONAL] tx ty tz
Define translation transformation (added AFTER rotation). If the keyword FRACTIONAL is present, the translation is assumed to be in fractional coordinates, otherwise orthogonal Angstroms. The subkey INVERT causes the inverse transformation to be applied. Note that an INVERT instruction if present will apply to both ROTATE & SHIFT.
TRANSFORM [INVERT] [FRACTIONAL] r11 r12 r13
r21 r22 r23 r31 r32 r33 tx ty tz
|maximum_shift||maximum shift (Angs) |
defaults to 0.2 Angs, fails if greater than 0.5 Angs
|CHAIN||act on only specified chain(s) |
eg   NOISE 0.1 CHAIN C   select only chain C
|BFACTOR [<minimum_B>]||act on only atoms with B-factor greater than <minimum_B>|
|PICK||act on only specified atom names |
eg   NOISE 0.1 PICK CA   to choose C-alpha only
Note that the atomname is case-sensitive
Phil Evans, MRC LMB, Cambridge, September 1992
######################## 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