usage: readArchive.pl archivefile options: [-showheader] [-inx index[:to]] [-step n] [-pdb template] [-xtract] [-prefix name] [-listfiles] [-center] [-fit ref] [-ensdir dir] [-ens tag] [-at inx] [-apply cmd] [-rms CA|CAB|C|O|N|side|back|all ... ref] [-qscore ref]Show source
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
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
- usage information
- output header information for archive file
- -inx from:to
- specify frame indices
- -step value
- skip frames according to the given value
- -pdb template
- use PDB structure as template
- extract PDB structures
- -prefix name
- file name prefix for extracted structures
- write file names of extracted PDB structures to standard output
- center each structure at the origin
- -fit ref
- fit each structure to a reference PDB structure
- -ensdir dir
- store each structure in the given ensemble directory name
- -ens tag
- store each structure in an ensemble using the given tag name
- -at inx
- specify ensemble index for extracting structures from archive
- -apply cmd
- apply specified command to each structure
- -rms CA|CAB|C|O|N|side|back|all ... ref
- calculate the root mean square deviation for each structure
- -qscore ref
- calculate Q-scores with respect to reference structure
readArchive.pl -inx 2 chain.archive
extracts the second entry from the archive file chain.archive
38 50 49 45 49 44 45 49 45 49 46 42 49 43 45 49 44 42 52 48 43 51 47 48 50 44 46 54 ...
readArchive.pl -showheader chain.archive
shows the header information for the archive file chain.archive
data length: 653 data items : 2 file type : 0 aux : 0
readArchive.pl -pdb 1vii.sample.1.pdb -inx 5 pdb.archive
extracts the fifth PDB coordinate entry from the archive file pdb.archive. The PDB file 1vii.sample.1.pdb is used as a template.
ATOM 1 HT1 MET 1 -11.034 -12.374 11.978 1.00 0.00 PRO0 ATOM 2 HT2 MET 1 -9.423 -11.987 11.814 1.00 0.00 PRO0 ATOM 3 N MET 1 -10.248 -12.354 11.297 1.00 0.00 PRO0 ATOM 4 HT3 MET 1 -10.153 -13.357 11.040 1.00 0.00 PRO0 ATOM 5 CA MET 1 -10.374 -11.444 10.219 1.00 0.00 PRO0 ATOM 6 CB MET 1 -11.529 -10.584 10.673 1.00 0.00 PRO0 ATOM 7 CG MET 1 -11.925 -9.404 9.777 1.00 0.00 PRO0 ATOM 8 SD MET 1 -13.320 -8.494 10.360 1.00 0.00 PRO0 ATOM 9 CE MET 1 -14.437 -9.388 9.361 1.00 0.00 PRO0 ATOM 10 C MET 1 -9.103 -10.663 10.088 1.00 0.00 PRO0 ...
readArchive.pl -pdb 1vii.sample.1.pdb -xtract -inx 1:4 -prefix 1vii -listfiles pdb.archive
extracts the first four coordinate records and creates the following files with the given prefix 1vii
1vii1.pdb 1vii2.pdb 1vii3.pdb 1vii4.pdb
readArchive.pl -pdb 1vii.sample.1.pdb -inx 1:4 -ens 1vii -ensdir ens pdb.archive
extracts the first four coordinate records and stores them in an ensemble data structure
readArchive.pl -pdb 1vii.sample.1.pdb -apply "rms.pl -fit 1vii.sample.1.pdb" -inx 1:4 pdb.archive
calculates the RMSD between each of the first four coordinate entries and the structure in 1vii.sample.1.pdb
0.0000 all 13.2677 all 10.9602 all 8.4937 all