PDBCUR (CCP4: Supported Program)

NAME

   pdbcur  -  a  curation  tool  providing  various analyses and
   manipulations of PDB files

SYNOPSIS

   pdbcur xyzin foo_in.pdb xyzout foo_out.pdb
   [Key-worded input file]

DESCRIPTION

   pdbcur provides various functions for analysing and manipulating
   the contents of PDB files. The program is written using the new
   MMDB  library  for  coordinate  data,  and  thus works with a
   hierarchical view of the atomic model. This hierarchy is visible
   for example in the atom selection syntax used.

   The program works on each keyword in turn. Therefore, the behaviour
   of a keyword may depend on what keywords have been previously
   applied, and how they have updated the model. In complex cases, it
   may be better to perform several runs of pdbcur.

INPUT AND OUTPUT FILES

  XYZIN

   Input coordinate file.

  XYZOUT

   Output coordinate file.

KEYWORDED INPUT

  summarise

   Summarise the contents of the coordinate file. For each chain in
   each model, the following information is listed:
     * The total number of residues
     * The set of residue ranges
     * The number of residues which have alternative conformations
     * The amino acid composition

  delsolvent

   Delete all solvent residues from all chains and all models. The
   list   of   residues  identified  as  "solvent"  is  kept  in
   $CCP4/lib/src/mmdb/mmdb_tables.cpp as array StdSolventName, and is
   currently "ADE", "CYT", "GUA", "INO", "THY", "URA", "WAT", "HOH",
   "TIP", "H2O", "DOD", "MOH".

   If a chain has both protein and solvent, only solvent gets removed.
   If a chain becomes empty after removal of solvent, it gets removed.

  delhydrogen

   Delete  all hydrogens in the model. This is simple wrapper to
   delatom.

  mostprob [ <altID> ]

   Keep only the most probable alternate conformation, i.e. that with
   the highest occupancy, irrespective of ordering and altID label.
   Other conformations are deleted from the model. For the kept atoms,
   the occupancy is set to 1.0 and the altID removed. Note that the
   resetting of occupancies renders a subsequent 'cutocc' keyword
   ineffective.

   If there are two conformations with occupancy of 0.5, then the
   conformation with alternate ID <altID> is kept. If this parameter
   is not given, it defaults to "A". Note that this only applies to
   equal dual conformers - for unequal conformers, that with the
   highest occupancy is kept, as explained above.

   This option is useful for switching back and forth between single
   and multiple conformers during refinement to check the validity of
   the model, and for generating single models for simulation or
   modelling.

  cutocc {cutoff}

   Delete all atoms with an occupancy less than or equal to {cutoff}.
   The default cutoff is 0.0, i.e. specifying cutocc with no arguments
   removes all atoms with zero occupancy.

  noanisou

   Removes all the ANISOU records from the coordinate file.

  renchain {selection of chain(s)} 'new chain ID'

   Example: renchain /*/A 'B'
   Quotations are optional and are useful for designation 'no chain
   ID'.
   Examples:
     * rename A to 'no chain ID': renchain A ''
     * rename 'no chain ID' to B: renchain /*// B

  renresidue {selection of residue(s)} 'new residue name'

   Example: renresidue (ALA) 'AL1'

  renatom {selection of atom(s)} 'new 4-letter atom name'

   Example: renatom CA[C] ' CC '

  renelement {selection of atom(s)} 'new element name'

   Example: renelement CA[C] 'AL'

  delmodel {selection of model(s)}

   Deletes the specified model(s).
   Example (delete model #1): delmodel /1
   Example (delete all models with chain A): delmodel /*/A

  delchain {selection of chain(s)}

   Deletes the specified chain(s).
   Example (delete chain A in all models): delchain A
   Example (delete chain A in 1st model): delchain /1/A

  delresidue {selection of residue(s)}

   Deletes the specified residue(s).
   Example (delete residues 33 to 120): delresidue 33-120

  delatom {selection of atom(s)}

   Deletes the specified atom(s).
   Example (delete all C-gamma atoms): delatom CG[C]

  deldist <x> <y> <z> <R>

   Deletes atoms within R angstrom of x,y,z.
   Example: deldist 32.1 45.6 -0.4 10.0

  lvmodel {selection of model(s)}

   Leaves the specified model(s), everything else is deleted.
   Example (leave only model #1): lvmodel /1
   Example (leave all models with chain A): lvmodel /*/A

  lvchain {selection of chain(s)}

   Leaves the specified chain(s), everything else is deleted.
   Example (leave chains A in all models): lvchain A
   Example (leave only chain A in 1st model): lvchain /1/A

  lvresidue {selection of residue(s)}

   Leaves the specified residue(s), everything else is deleted.
   Example (leave residues 33.A to 120.B): lvresidue 33.A-120.B

  lvatom {selection of atom(s)}

   Leaves the specified atom(s), everything else is deleted.
   Example (leave only C-alpha atoms): lvatom "CA[C]:*"
   Note the use of * to get all alternative conformations, since the
   default for atom-level selection is a blank alt loc indicator only,
   see atom selection syntax.

  lvdist <x> <y> <z> <R>

   Leaves  atoms  within R angstrom of x,y,z; everything else is
   deleted.
   Example: lvdist 32.1 45.6 -0.4 10.0

  write {PDB|CIF|BIN}

   Writes 'xyzout' as a PDB, mmCIF or MMDB BINary file. By default,
   the file is written in the format of input file.

  genter

   No parameters; this keyword generates PDB 'TER' cards.

  sernum

   No parameters; this keyword generates correct atom serial numbers.

  mvsolvent

   No parameters; moves solvent chains to the end of models.

  symmetry <spgname>

   Input of the space group symmetry name, e.g. 'P 21 21 21' (without
   quotation marks, spaces _are_ significant, case sensitive). This
   parameter is mandatory if coordinate file does not specify the
   space group symmetry.

  geometry <a> <b> <c> <alpha> <beta> <gamma>

   Input of the unit cell dimensions (space-separated real numbers).
   This parameter is mandatory if coordinate file does not specify the
   cell parameters.

  genunit

   Generating a unit cell as defined by crystallographic information
   given in coordinate file or set up with keywords 'symmetry' and
   'geometry'. Chains generated by identity operation retain their
   names,  all  other are renamed as c_n, where c is the chain's
   original name, and n is the number of symmetry operation in the
   space group used (starting from 0 for identity operation on). In
   order to comply with PDB standards, the chains are then to be
   renamed using renchain command, e.g. renchain A_2 H . The chains
   may be assigned automatically generated 1-character names using the
   command mkchainIDs .

   Example: rnase.pdb contains 2 chains A and B. Generate a unit cell,
   space group P 21 21 21, 4 symmetry operations, and assign chain IDs
   C,D,E for chain A transformed by operations #1,2,3, and IDs F,G,H
   for chain B transformed by the same operations. Chains A and B
   transformed by 0th operation (identity) retain their IDs:

pdbcur xyzin rnase.pdb xyzout ucell.pdb <<eof
? symm P 21 21 21
? genu
? renc A_1 C
? renc A_2 D
? renc A_3 E
? renc B_1 F
? renc B_2 G
? renc B_3 H
? eof

  symop X,Y,Z 'old chain ID' 'new chain ID' 'old ID' 'new ID' ...

   Declares (but does not apply) a symmetry operation. The symmetry
   operations for each X,Y,Z fractional coordinates must be written
   without spaces. Pairs 'old chain ID' - 'new chain ID' specify how
   the chains should be renamed after operation. This input is not
   mandatory. If no renaming is specified, the newly generated chains
   will be renamed automatically (see keyword symcommit).

   Example: symop Y+1/2,X-1/2,Z A S B R
   (declare  symmetry  transformation x=Y+1/2, y=X-1/2, z=Z with
   renaming chain A to S and B to R.

  symcommit

   No parameters.
   Applies all symmetry operations declared since last symcommit
   statement. First operation (normally identity) will be applied to
   the existing set of coordinates, all other will be applied to the
   duplicates of the coordinates, and the results are merged.

   The  newly  generated chains are named as C_n, where C is the
   original  chain name, and n is the symmetry operation number.
   Symmetry  operations  are  numbered  as  they appear in symop
   statements, from 0 on; however the very first one is applied to the
   existing chains, which are not renamed in this case.

   Example:

pdbcur xyzin rnase.pdb xyzout rnase1.pdb <<eof
? symop  X,Y,Z
? symop  Y+1/2,X-1/2,Z
? symcommit
? eof

   just adds two chains named A_1 and B_1, obtained according to the
   rule Y+1/2,X-1/2,Z from chains A and B, to the existing file.

  mkchainIDs

   Automatically  generates 1-character chain IDs after applying
   symmetry operations. The IDs are generated such that they use all
   available letters starting from A, and a chain is not renamed if
   its name is already a 1-character one.

   The following example

pdbcur xyzin rnase.pdb xyzout ucell.pdb <<eof
? symm P 21 21 21
? genu
? mkch
? eof

   produces exactly the same result as that given for keyword GENUNIT,
   because the original chains are named sequentially as A,B (not G,I,
   for example).

  rotate {selection of atoms} alpha beta gamma x y z

  rotate {selection of atoms} alpha beta gamma center

   Euler rotation of selected atoms through angles alpha, beta and
   gamma (degrees) as applied to the initial Z-axis, new Y-axis and
   newest Z-axis, correspondingly. The rotation center is given by
   either orthogonal coordinates x, y and z or by keyword 'center' for
   specifying the mass center of the selected atoms.

   Examples:

 1. 90-degree rotation of chain A about Z-axis in
    original coordinate system:
    rotate   A   90 0 0   0 0 0
 2. 60-degree rotation of chains A and B about Y-axis
    in the coordinate system of their mass center:
    rotate 'A,B'  0 60 0   center

  translate {selection of atoms} frac tx ty tz

  translate {selection of atoms} orth tx ty tz

   Translate  selected  atoms  through tx ty tz, which can be in
   fractional or orthogonal coordinates, depending on subkeyword
   'frac' or 'orth'.

  vrotate {selection of atoms} alpha vx vy vz x y z

  vrotate {selection of atoms} alpha vx vy vz center

  vrotate {selection of atoms} alpha atom1 atom2

   Rotation of selected atoms through angle alpha (degrees) about a
   vector given by direction (vx,vy,vz) from the rotation center
   (given as x,y,z or by keyword 'center' for the mass center of the
   selected atoms). The vector may also be specified by two atoms
   atom1 and atom2 represented in the mmdb selection notation.

   Examples:

 1. 90-degree rotation of chain A about Z-axis in
    original coordinate system:
    vrotate  A   90  0 0 1   0 0 0
 2. 60-degree rotation of chains A and B about Y-axis
    in the coordinate system of their mass center:
    vrotate 'A,B'  60  0 1 0  center
 3. 45-degree rotation of all atoms about vector connecting
    C-alpha atoms of residues 20.A of chain A and 55
    of chain B:
    vrotate /*/*/*/* 45  /1/A/20.A/CA[C] /1/B/55/CA[C]
    or, if there is only one model in the PDB file:
    vrotate *  45  A/20.A/CA[C] B/55/CA[C]

ATOM SELECTION SYNTAX

   Specification of the selection sets:

   either
          /mdl/chn/s1.i1-s2.i2/at[el]:aloc

   or
          /mdl/chn/*(res).ic/at[el]:aloc

   where no spaces are allowed. The slashes separate the hierarchical
   levels of models, chains, residues and atoms.

   Notations:

 mdl   - the model's serial number or 0 or '*' for any model
         (default).
 chn   - the chain ID or list of chain IDs like 'A,B,C' or
         '*' for any chain (default).
 s1,s2 - the starting and ending residue sequence numbers
         or '*' for any sequence number (default).
 i1,i2 - the residues insertion codes or '*' for any
         insertion code. If the sequence number other than
         '*' is specified, then insertion code defaults to ""
         (no insertion code), otherwise the default is '*'.
 res   - residue name or list of residue names like 'ALA,SER'
         or '*' for any residue name (default)
 at    - atom name or list of atom names like 'CA,N1,O' or
         '*' for any atom name (default)
 el    - chemical element name or list of chemical element
         names like 'C,N,O', or '*' for any chemical element
         name (default)
 aloc  - the alternative location indicator or list of
         alternative locations like 'A,B,C', or '*' for any
         alternate location. If the atom name and chemical
         element name is specified (both may be '*'), then
         the alternative location indicator defaults to ""
         (no alternate location), otherwise the default is
          '*'.

   Values for chain IDs, residue names, atom names, chemical element
   names and alternative location indicators may be negated by prefix
   '!'. For example, '!A,B,C' for the list of chain names means 'any
   chain ID but A,B,C'.

   Generally, any hierarchical element as well as the selection code
   may be omitted, in which case it is replaced for default (see
   above). This makes the following examples valid:

 *                   select all atoms
 /1                  select all atoms in model 1
 A,B                 select all atoms in chains A and B in
                     all models
 /*/1,2              select all atoms in chains 1 and 2 in
                     all models. Note that you must use this
                     format with numerical chain identifiers
 /1//                select all atoms in chain without chainID
                     in model 1
 /*/,A,B/            select all atoms in chain without chainID,
                     chain A and B in all models
 33-120              select all atoms in residues 33. to 120.
                     in all chains and models
 A/33.A-120.B        select all atoms in residues 33.A to
                     120.B in chain A only, in all models
 A/33.-120.A/[C]     select all carbons in residues 33. to
                     120.A in chain A, in all models
 CA[C]               select all C-alphas in all
                     models/chains/residues
 A//[C]              select all carbons in chain A, in all models
 (!ALA,SER)          select all atoms in any residues but
                     ALA and SER, in all models/chains
 /1/A/(GLU)/CA[C]    select all C-alphas in GLU residues of
                     chain A, model 1
 /1/A/*(GLU)./CA[C}: same as above
 [C]:,A              select all carbons without alternative
                     location indicator and carbons in alternate
                     location A

   NOTE: if a selection contains comma(s), the selection sentence must
   be embraced by quotation marks, which indicate to the input parser
   that the sentence is a single input parameter rather than a set of
   comma- separated arguments.

PROGRAM OUTPUT

   The program currently gives a short summary of the operations
   carried out.

EXAMPLES

  Runnable example

   pdbcur.exam

SEE ALSO

   ncont - MMDB application for finding contacts.
   pdbset - traditional PDB utility program.

AUTHORS

   Eugene Krissinel, European Bioinformatics Institute, Cambridge, UK.
   Martyn Winn, Daresbury Laboratory, UK - some additional keywords.