pdb-get [-pdbdir dir] [-pdbmoddir dir] [-pdbcamoddir dir] [-cat] [-ca-mod] [-nofetch] pdbid
Get the path to a PDB file. If the file already exists in the specified
PDB directory, it is used, otherwise the file is downloaded. The resulting
file will be named in the form ${pdbid}.pdb.gz
and will always be gzipped.
A search will be done for the file, checking PDB both current and the obsolete
databases.
-pdbdir dir -
Specifies an alternate PDB directory. The default is
/projects/compbio/data/pdb.
-pdbmoddir dir -
Specified a directory that will be checked for modified
PDB files. A file here overrides the file in -pdbdir. The default is
/projects/compbio/data/pdb-modified.
-pdbcamoddir dir -
Specified a directory that will be checked for MAXSPROUT
modified C-alpha-only PDB files. The default is
/projects/compbio/data/pdb-ca-mod.
Only used if -ca-mod is specified.
Files are check for under both the 1grl.brk_ca_mod.gz and 1grl.pdb.gz
names in this directory.
-ca-mod -
Check for MAXSPROUT C-alpha modified files. These files will not
be fetched, they must be installed in the pdb-ca-mod
directory. They are availabled from
ftp://ftp.ebi.ac.uk/pub/databases/camodpdb/.
-cat -
Instead of returning the file name, uncompress the file to stdout.
-nofetch -
If specified, don't fetch the file if it doesn't exist.
Outputs the name of the file that would be downloaded.
pdbid -
PDB four character identifier of the file to get. Trailing chain
identifiers and other garbage is dropped. Maybe upper or lower case.
-cat is specified is written to stdout.
If an error occurs, a message is written to stderr.
This idea is that the output of this script is used to get the file name to
open or to the actual data stream.
For example:
pdb-get -cat 1ceo | egrep '^SHEET'
rasmol `pdb-get 1ceo`