MMTSB
Tool Set Documentation

readArchive.pl

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Usage

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]
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Description

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.

Options

-help 
usage information
-showheader 
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
-xtract 
extract PDB structures
-prefix name 
file name prefix for extracted structures
-listfiles 
write file names of extracted PDB structures to standard output
-center 
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

Examples

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