BMERC : needle tools : Programs : ATOM programs
Presently, the only "general" PDB ATOM tool is filter-pdb-atoms.pl, which is used by many tools to do preprocessing and consistency checking of PDB ATOM records.
filter-pdb-atoms.pl [-locus string] [-chains chain-spec] [-new-chain-id letter] [-output [all | backbone | cb]] [-pass-through [chain | all]] [-hcb | -hcb-all] [-ala] [-residue-index-file rif-file-name] [-include-hetatms HET ...] [-exclude-hetatms HET ...] [-print-peptide-length-histogram] [ pdb-file-name ]If pdb-file-name is not specified, or is specified as "-", then the standard input is used. The selected ATOM, TER, and possibly other records (depending on options) are sent to the standard output.
If you just want to find out what's going on with a given PDB file, here's a quick hack that does the trick:
filter-pdb-atoms.pl 3dfr.ent > /dev/nullThis gives you all the warnings with none of the atoms (since the warnings go to stderr, and the atoms to stdout). This is also the easiest way to use the -print-peptide-length-histogram option.
460c460 < ATOM 719 CB GLY 1 92 34.872 -7.279 128.363 1.00 8.88 1BBT 999 --- > ATOM 0 CB GLY 1 92 34.872 -7.083 128.812 0.00 0.00[The all-perl version in Release 1.0 comes closer to the original, but is still significantly off. Here we have the first filter-pdb-atoms.pl version versus the current version:
725c725 < ATOM 0 CB GLY 1 92 34.872 -7.083 128.812 0.00 0.00 C --- > ATOM 0 CB GLY 1 92 34.872 -7.233 128.468 0.00 0.00 C1pgs also has a large CB GLY variation. Probably not worth worrying about. -- rgr, 22-Aug-97.]