fixatname (1) - correct AMBER pseudo-PDB files so they are in standard PDB format

FIXATNAME(1)

NAME

fixatname - correct AMBER pseudo-PDB files so they are in standard PDB format

SYNOPSIS

fixatname [ file1 ... ]

DESCRIPTION

Versions of AMBER prior to version 3.0 revision A produced PDB files that had atom names aligned in the wrong columns (see MidasPlus User's Manual, Part III, Protein Data Bank Format for details of PDB format). Fixatname corrects this misalignment. AMBER PDB files have their atom names left- adjusted in columns 13-16 of each line. Fixatname left- adjusts the atom name in columns 14-16, with the former contents of column 16 being placed in column 13. This results in atom names that conform to the PDB standard with the rather infrequent exception of atom names with a two- character atomic symbol (such as iron, FE). Such cases can be corrected by hand after processing by fixatname.

Fixatname reads from standard input if no file names are specified. Fixatname prints the corrected PDB file on standard output.

BUGS

Atoms with two-character atomic symbols are misaligned, as mentioned above.

AUTHOR

Conrad Huang

UCSF Computer Graphics Laboratory