pdbconvert Command Help

Command: $SCHRODINGER/utilities/pdbconvert

 Options for PDB import:
  -model <number>       : convert a PDB input model other than the first listed
  -num_models <number>  : specify the number of input models to be converted
  -no_color             : color atoms by type, not "error code"
  -no_dup_conect        : do not interpret duplicate CONECT records as 
                          multiple bonds
  -no_geometry          : don't add additional bonds by geometry, and
                          only use CONECT records to assign bonds.
  -no_fixelem           : don't attempt to recognize branch codes in names
                          like 'AC3*' or 'NN7 ', so that the proper element
                          can be determined.
  -hybrid36             : hybrid36 scheme for serial numbers (default)
  -hex                  : hex encoding for atom serial numbers
                          after 99999 and residue numbers after 9999
  -histidine <mode>     : HIS protonation mode when residue lacks hydrogens
                           protonation <mode> is one of:
                            delta      : only ND1; neutral residue (default)
                            epsilon    : only NE2; neutral residue
                            protonated : both ND1 and NE2; +1 total res charge
  -occ <sites>          : For atoms with alternate sites with different 
                          occupation factors, specify which to read.
                           <sites> is one of:
                            all        : read all alternate sites (default)
                            first      : read first occ site listed per atom
  -first_occ            : equivalent to -occ first
  -all_occ              : equivalent to -occ all
  -charge <mode>        : Termini protonation <mode>, one of:
                            ph7_protonate_caps : protonate termini, identified
                                    from SEQRES records if available (default)
                            neutral            : do not add formal charges
  -use_component_dict   : use residue information from component dictionary 
  -no_component_dict    : don't use residue information from component 
                          dictionary (default) 
  -noindex              : On pdb->mae conversion don't update the indexing
                          properties to store the index of file on conversion.
                          By default it stores source file and structure index.
  -strict_resname       : Read the residue name only from 18-20 columns of pdb record.
                          By default, 18-21 columns are usually read.

 Options for PDB export only:
  -n <structs>          : specify a comma delimited series of colon separated
                          ranges and single values to convert.  For example:
                          1:10,14  (structures 1 through 10 and 14
                          2:       (structure 2 through end of file)
                          :5,13:18 (structure 1 through 5, and 13 through 18)
                          If the structures are not conformers, then converted
                          PDB structures will be written to separate files as
                          foo-01.pdb, foo-02.pdb, etc. given '-opdb foo.pdb'
  -no_dup_conect        : do not write duplicate CONECT records to represent
                          multiple bonds
  -no_renum             : retain atom indices from the input Maestro/MMod file
  -no_reorder           : retain atom indices from the input Maestro/MMod file
  -reorder_by_resnum    : Write ordered PDB by residue number
  -reorder_by_sequence  : Write ordered PDB by sequence
  -psp                  : Treat psp residues as standard residues for sorting
  -no_translate_pdb_resnames : do not translate pdb residue names to a                                         standard set while writing
  -write_seq_headers    : write SEQRES, HELIX, SHEET, TURN and SSBOND records 
  -brief                : write only ATOM, HETATM, CONECT, title and 
                          PDB version (REMARK 4) records
  -write_multiple_structs_as_models 
                        : write multiple non conformer structures as multiple 
                          MODELs. This results in a non standard pdb file and 
                          is strongly discouraged.

 
pdbconvert [options] -i<format> input-file -o<format> output-file

 <format>:
  pdb                   : PDB format (can be gzipped)
  mae                   : Maestro format (can be gzipped)