This utility is used to extract data from archive files. Archive files are written during replica exchange simulations with aarex.pl or latrex.pl. They can also be generated manually with writeArchive.pl.
The option -showheader is available to display the contents of the archive header with information on the length of each entry, the total number of entries and the entry type.
There are a number of ways archive entries can be extracted. In the simplest form, an archive entry is selected by its index with the -inx option. If coordinates from a PDB file are stored in the archive, a PDB template file also needs to be given with the option -pdb. This template file is used to provide the atom and residue names while the coordinates are filled in from the data record in the archive file.
In order to extract more than record, the option -xtract may be used. In this case multiple records as indicated by a range of indices given with -inx are extracted into separate files. The prefix of these output files can be set with -prefix, and if the names of the files that are being created should be also written to standard output the option -listfiles. This may be useful for post processing with other tools where a list of files is expected as input.
A number of data record can also be checked in automatically into an ensemble data structure. In this case the option -ens is used with a tag name under which the structures are stored in the ensemble and a directory for the ensemble can be given with -ensdir. This option only works with coordinate entries and requires a PDB template given with -pdb.
Finally, it is possible to apply an external command directly to a set of coordinate entries which may be more convenient than extracting the entries to disk and then running the desired program. This is done with -apply followed by a command that is able to read a PDB file from standard input. More optimized is the calculation of coordinate RMS deviations and Q scores when the options -rms and -qscore are used.