convpdb.pl Show Source
convpdb.pl [options] [PDBfile]
options: [-center] [-translate dx dy dz]
[-rotate m11 m12 m13 m21 m22 m23 m31 m32 m33]
[-rotatex phi] [-rotatey phi] [-rotatez phi]
[-scale factor] [-diff PDBfile] [-difflsqfit] [-add PDBFile]
[-nmode file amplitude weight]
[-nmodesample file prefix from to delta] [-skipzero]
[-sel list] [-exclude list]
[-chain id] [-model num] [-nohetero]
[-selseq abbrev]
[-nsel Selection]
[-merge pdbfile]
[-renumber start] [-addres value]
[-renumwatersegs]
[-match pdbfile]
[-setchain id]
[-readseg] [-chainfromseg]
[-charmm19] [-amber]
[-out charmm19 | charmm22 | amber | generic]
[-segnames]
[-fixcoo]
[-ssbond res1:res2[=res1:res2]] [-nossbond]
[-solvate] [-cutoff value]
[-octahedron] [-cubic]
[-ions NAME:num[=NAME:num]]
[-info]
[-fill inx:seq]
[-mol2]
[-cleanaux] [-removeclashes]

Converts and manipulates a protein structure PDB file. The input is read through standard input or from a file given as a command line argument. With the option -renumber renumbering of the residues can be requested to obtain continuous residue numbering starting from a given number. Alternatively, the option -add adds a constant to every residue number for the case of missing residues in the PDB file when continuous renumbering would not be desirable. As a third option the residue numbering may be adjusted to match the numbering in a reference PDB file given with -match by searching for the best sequence match.

If the input PDB file comes from CHARMM with the CHARMM19 force field the option -charmm19 needs to be specified to correctly identify histidine residues. Output is written by default for the CHARMM22 protein force field but the format can be selected with the -out option. Possible values are charmm19, charmm22, amber, and generic. With the generic option all histidine residues as named HIS regardless of the name or protonation state in the input file. It is also possible to append noh to the format name to request exclusion of all hydrogen atoms in the output.
The molecule can be centered at the origin with -center or shifted with -translate dx dy dz.

With -sel followed by a list of residues can be used to select a subset of residues. This may be done, e.g., for loop modeling applications where only the neighborhood of the loop under consideration is needed for modeling. This option is complemented by -merge for merging a template structure from a PDB file with another PDB file. Again, this functionality is particularly useful for loop modeling in order to reassemble a complete protein structure if only the loop vicinity is being used during modeling. Alternatively, one may also specify a list of residues with -exclude that should be excluded from the output.

A structure fragment can also be selected based on its amino acid sequence given with the option -selseq. The sequence has to match exactly part of the sequence of the input structure for this option to work and only a single fragment can be extracted at a time.

For multidomain structures the option -chain is available to select a particular chain. The chain ID may be set or changed with -setchain.

Files from the PDB data bank often contain residues in addition to a biomolecule of interest such us solvent or small ligands. They are usually denoted with HETATM records. The option -nohetero is available to ignore such atoms when a PDB structure is read.

A few options are available to handle CHARMM segment names. If -readseg is given, the CHARMM segment names are read from the output. The option -chainfromseg is available to set chain IDs from the last letter of the segment names.
With -segnames segment names are included in the output file. Segement IDs are necessary for using a PDB file with CHARMM. Unless they have been read from the input file they are generated automatically if this option is given.

The option -fixcoo can be used to ensure reasonable c-terminal oxygen coordinates. If the second terminal oxygen is missing or has incorrect coordinates it will be rebuilt correctly with this option.

If SSBOND records are present in the input file to indicate the presence of disulfide bonds, they are maintained. The option -nossbond is available to suppress SSBOND records. In order to add disulfide bonds to a PDB file, the option -ssbond may be used with a list of cystine residue pairs.

Finally, this script can be used to solvate the input PDB structure in a rectangular (default), cubic, or octahedrol box of pre-equilibrated water molecules. This is possible with the option -solvate. The type of box is selected with -cubic or -octahedron. A cutoff value may be specified with -cutoff to indicate the minimum margin from the molecule that is being solvated to the edge of the box.
convpdb.pl -out charmm19 1vii.orig.pdb
converts the input PDB file (from the PDB databank) to a format suitable for the CHARMM19 force field. 
ATOM      1  N   MET    41       1.177 -10.035  -3.493  1.00  0.00          
ATOM      2  CA  MET    41       0.292  -8.839  -3.377  1.00  0.00          
ATOM      3  C   MET    41      -0.488  -8.912  -2.063  1.00  0.00          
ATOM      4  O   MET    41      -1.039  -9.937  -1.709  1.00  0.00          
ATOM      5  CB  MET    41      -0.674  -8.793  -4.565  1.00  0.00          
ATOM      6  CG  MET    41      -0.091  -7.889  -5.657  1.00  0.00          
ATOM      7  SD  MET    41      -0.153  -8.747  -7.255  1.00  0.00          
ATOM      8  CE  MET    41      -0.971  -7.432  -8.193  1.00  0.00          
ATOM      9 1H   MET    41       0.835 -10.784  -2.856  1.00  0.00          
ATOM     10 2H   MET    41       1.166 -10.381  -4.475  1.00  0.00          
ATOM     11 3H   MET    41       2.149  -9.775  -3.227  1.00  0.00          
ATOM     12  HA  MET    41       0.900  -7.946  -3.376  1.00  0.00          
ATOM     13 1HB  MET    41      -0.814  -9.790  -4.956  1.00  0.00          
ATOM     14 2HB  MET    41      -1.623  -8.395  -4.242  1.00  0.00          
ATOM     15 1HG  MET    41      -0.664  -6.978  -5.716  1.00  0.00          
...
convpdb.pl -renumber 1 -out charmm22noh -segnames 1vii.orig.pdb
converts the input PDB file (from the PDB databank) to a format suitable for CHARMM22. Hydrogen atoms are not included in the output and residues are renumbered to start at 1. Segment ID are generated and included in the output. 
ATOM      1  N   MET     1       1.177 -10.035  -3.493  1.00  0.00      PRO0
ATOM      2  CA  MET     1       0.292  -8.839  -3.377  1.00  0.00      PRO0
ATOM      3  C   MET     1      -0.488  -8.912  -2.063  1.00  0.00      PRO0
ATOM      4  O   MET     1      -1.039  -9.937  -1.709  1.00  0.00      PRO0
ATOM      5  CB  MET     1      -0.674  -8.793  -4.565  1.00  0.00      PRO0
ATOM      6  CG  MET     1      -0.091  -7.889  -5.657  1.00  0.00      PRO0
ATOM      7  SD  MET     1      -0.153  -8.747  -7.255  1.00  0.00      PRO0
ATOM      8  CE  MET     1      -0.971  -7.432  -8.193  1.00  0.00      PRO0
ATOM     20  N   LEU     2      -0.523  -7.832  -1.331  1.00  0.00      PRO0
ATOM     21  CA  LEU     2      -1.241  -7.824  -0.028  1.00  0.00      PRO0
ATOM     22  C   LEU     2      -2.736  -8.045  -0.241  1.00  0.00      PRO0
ATOM     23  O   LEU     2      -3.467  -7.134  -0.574  1.00  0.00      PRO0
ATOM     24  CB  LEU     2      -1.019  -6.479   0.660  1.00  0.00      PRO0
ATOM     25  CG  LEU     2      -0.044  -6.671   1.819  1.00  0.00      PRO0
ATOM     26  CD1 LEU     2       1.375  -6.825   1.270  1.00  0.00      PRO0
...
convpdb.pl -sel 10:21 1vii.exp.pdb
copies only residues 10 through 21 from the input PDB file to the output. 
ATOM    141  N   VAL    10      -1.787  -4.543   8.123  1.00  0.00          
ATOM    142  CA  VAL    10      -0.514  -3.998   7.587  1.00  0.00          
ATOM    143  C   VAL    10      -0.582  -2.467   7.545  1.00  0.00          
ATOM    144  O   VAL    10      -0.049  -1.793   8.404  1.00  0.00          
ATOM    145  CB  VAL    10      -0.291  -4.552   6.183  1.00  0.00          
ATOM    146  CG1 VAL    10       0.935  -3.888   5.559  1.00  0.00          
ATOM    147  CG2 VAL    10      -0.064  -6.066   6.275  1.00  0.00          
ATOM    148  H   VAL    10      -2.636  -4.140   7.863  1.00  0.00          
ATOM    149  HA  VAL    10       0.303  -4.301   8.225  1.00  0.00          
ATOM    150  HB  VAL    10      -1.160  -4.352   5.575  1.00  0.00          
ATOM    151 1HG1 VAL    10       1.011  -2.867   5.904  1.00  0.00          
ATOM    152 2HG1 VAL    10       1.818  -4.433   5.850  1.00  0.00          
ATOM    153 3HG1 VAL    10       0.843  -3.900   4.483  1.00  0.00          
ATOM    154 1HG2 VAL    10      -0.725  -6.484   7.019  1.00  0.00          
ATOM    155 2HG2 VAL    10      -0.266  -6.521   5.318  1.00  0.00          
...
convpdb.pl -match 1vii.shift.pdb 1vii.exp.pdb
matches the residue numbering of the input file with the numbering in 1vii.shift.pdb after aligning both sequences. 
ATOM      1  N   MET     6       1.177 -10.035  -3.493  1.00  0.00          
ATOM      2  CA  MET     6       0.292  -8.839  -3.377  1.00  0.00          
ATOM      3  C   MET     6      -0.488  -8.912  -2.063  1.00  0.00          
ATOM      4  O   MET     6      -1.039  -9.937  -1.709  1.00  0.00          
ATOM      5  CB  MET     6      -0.674  -8.793  -4.565  1.00  0.00          
ATOM      6  CG  MET     6      -0.091  -7.889  -5.657  1.00  0.00          
ATOM      7  SD  MET     6      -0.153  -8.747  -7.255  1.00  0.00          
ATOM      8  CE  MET     6      -0.971  -7.432  -8.193  1.00  0.00          
ATOM      9 1H   MET     6       0.835 -10.784  -2.856  1.00  0.00          
ATOM     10 2H   MET     6       1.166 -10.381  -4.475  1.00  0.00          
ATOM     11 3H   MET     6       2.149  -9.775  -3.227  1.00  0.00          
ATOM     12  HA  MET     6       0.900  -7.946  -3.376  1.00  0.00          
ATOM     13 1HB  MET     6      -0.814  -9.790  -4.956  1.00  0.00          
ATOM     14 2HB  MET     6      -1.623  -8.395  -4.242  1.00  0.00          
ATOM     15 1HG  MET     6      -0.664  -6.978  -5.716  1.00  0.00          
...
convpdb.pl -merge 1vii.exp.pdb 1vii.sel10:21.pdb
merges the fragment in 1vii.sel10:21.pdb with the structure in 1vii.exp.pdb. 
ATOM      1  N   MET     1       1.177 -10.035  -3.493  1.00  0.00      PRO0
ATOM      2  CA  MET     1       0.292  -8.839  -3.377  1.00  0.00      PRO0
ATOM      3  C   MET     1      -0.488  -8.912  -2.063  1.00  0.00      PRO0
ATOM      4  O   MET     1      -1.039  -9.937  -1.709  1.00  0.00      PRO0
ATOM      5  CB  MET     1      -0.674  -8.793  -4.565  1.00  0.00      PRO0
ATOM      6  CG  MET     1      -0.091  -7.889  -5.657  1.00  0.00      PRO0
ATOM      7  SD  MET     1      -0.153  -8.747  -7.255  1.00  0.00      PRO0
ATOM      8  CE  MET     1      -0.971  -7.432  -8.193  1.00  0.00      PRO0
ATOM      9 1H   MET     1       0.835 -10.784  -2.856  1.00  0.00      PRO0
ATOM     10 2H   MET     1       1.166 -10.381  -4.475  1.00  0.00      PRO0
ATOM     11 3H   MET     1       2.149  -9.775  -3.227  1.00  0.00      PRO0
ATOM     12  HA  MET     1       0.900  -7.946  -3.376  1.00  0.00      PRO0
ATOM     13 1HB  MET     1      -0.814  -9.790  -4.956  1.00  0.00      PRO0
ATOM     14 2HB  MET     1      -1.623  -8.395  -4.242  1.00  0.00      PRO0
ATOM     15 1HG  MET     1      -0.664  -6.978  -5.716  1.00  0.00      PRO0
...
convpdb.pl -sel 1:5=10:21 -setchain B -segnames 1vii.exp.pdb
extracts residues 1 through 5 and 10 through 21 from the input file. The chain ID is set to B and CHARMM segment names are generated in the output. 
ATOM      1  N   MET B   1       1.177 -10.035  -3.493  1.00  0.00      PR01
ATOM      2  CA  MET B   1       0.292  -8.839  -3.377  1.00  0.00      PR01
ATOM      3  C   MET B   1      -0.488  -8.912  -2.063  1.00  0.00      PR01
ATOM      4  O   MET B   1      -1.039  -9.937  -1.709  1.00  0.00      PR01
ATOM      5  CB  MET B   1      -0.674  -8.793  -4.565  1.00  0.00      PR01
ATOM      6  CG  MET B   1      -0.091  -7.889  -5.657  1.00  0.00      PR01
ATOM      7  SD  MET B   1      -0.153  -8.747  -7.255  1.00  0.00      PR01
ATOM      8  CE  MET B   1      -0.971  -7.432  -8.193  1.00  0.00      PR01
ATOM      9 1H   MET B   1       0.835 -10.784  -2.856  1.00  0.00      PR01
ATOM     10 2H   MET B   1       1.166 -10.381  -4.475  1.00  0.00      PR01
ATOM     11 3H   MET B   1       2.149  -9.775  -3.227  1.00  0.00      PR01
ATOM     12  HA  MET B   1       0.900  -7.946  -3.376  1.00  0.00      PR01
ATOM     13 1HB  MET B   1      -0.814  -9.790  -4.956  1.00  0.00      PR01
ATOM     14 2HB  MET B   1      -1.623  -8.395  -4.242  1.00  0.00      PR01
ATOM     15 1HG  MET B   1      -0.664  -6.978  -5.716  1.00  0.00      PR01
...
convpdb.pl -selseq AFANLPL 1vii.exp.pdb
extracts residues 17 through 23 corresponding to the sequence AFANLPL from the input file. 
ATOM    250  N   ALA    17      -6.563   3.127  -1.620  1.00  0.000         
ATOM    251  CA  ALA    17      -6.531   4.418  -0.879  1.00  0.000         
ATOM    252  C   ALA    17      -5.098   4.662  -0.409  1.00  0.000         
ATOM    253  O   ALA    17      -4.613   5.776  -0.400  1.00  0.000         
ATOM    254  CB  ALA    17      -7.464   4.346   0.332  1.00  0.000         
ATOM    255  H   ALA    17      -7.104   2.381  -1.285  1.00  0.000         
ATOM    256  HA  ALA    17      -6.842   5.221  -1.532  1.00  0.000         
ATOM    257 1HB  ALA    17      -7.940   3.377   0.364  1.00  0.000         
ATOM    258 2HB  ALA    17      -6.892   4.496   1.236  1.00  0.000         
ATOM    259 3HB  ALA    17      -8.218   5.115   0.254  1.00  0.000         
ATOM    260  N   PHE    18      -4.416   3.617  -0.022  1.00  0.000         
ATOM    261  CA  PHE    18      -3.006   3.761   0.443  1.00  0.000         
ATOM    262  C   PHE    18      -2.204   4.557  -0.585  1.00  0.000         
ATOM    263  O   PHE    18      -1.238   5.217  -0.260  1.00  0.000         
ATOM    264  CB  PHE    18      -2.397   2.371   0.590  1.00  0.000         
...
Molecule.pm  Analyze.pm
Michael Feig, Brooks group, TSRI