checkin.pl - Revision history

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Feig at 14:28, 12 August 2006

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__NOTOC__
== Usage ==

<mmtsbToolUsage cmd="checkin.pl"></mmtsbToolUsage>

== Description ==

This script is used to add PDB files or SICHO chain files to
an ensemble of protein structures. 
Ensembles are used in structure prediction to obtain statistically
meaningful energy scores for structural families
identified by clustering (see <docmark>cluster.pl</docmark>).
While a number of MMTSB tools directly generate ensembles from
running multiple lattice simulations and all-atom refinement
(<docmark>enslatsim.pl</docmark>, <docmark>ensmin.pl</docmark>),
or replica exchange sampling (<docmark>latrex.pl</docmark> and
<docmark>aarex.pl</docmark>) this script is intended to
setup an ensemble data structure from structures generated elsewhere
so that ensemble-based MMTSB tools can be used for structure evaluation
and refinement. 
Structure ensembles are stored in a directory tree with a separate
directory for each running index within the ensemble. Multiple
conformations for a given index are distinguished by tags. Structural
properties for all structures with a given tag are maintained in a
single database file in the top of the directory tree. It is not
recommended to modify the directory structure, add or remove files
manually, or edit property database files directly since a number
of different MMTSB tools rely on certain data structures and formats.
 
checkin.pl is called with a tag and one or more files to be
added to an ensemble. The list of files can also be read from an
external file (or standard input if - is given
as the file name) by using the -f option.
By default, the file(s) are added to an ensemble in the current directory
(a new ensemble is created if none exists). A different directory may
be specified with -dir. The option -at can be used to
replace structures starting at a given index rather than adding them.
The option -sicho is available to check in SICHO lattice chains
instead of PDB files. All-atom structures in PDB format are automatically
rebuilt from SICHO chains if a MONSSTER sequence file is available
(see: <docmark>genseq.pl</docmark>). If the name of the sequence file is
not available from the ensemble configuration files it may by given
with -seq. 
This script can also generate an ensemble from a binary CHARMM trajectory
file if it is run on the same computer platform as CHARMM when the
trajectory was created. In this case the option -dcd can be
used with a PDB template file, which has to have the correct matching
order and number of atoms corresponding to the trajectory file, and
the name of the trajectory file.-dcdskip can be used in addition
in order to skip conformations in the trajectory. 

== Options ==

; -help : usage information

== Examples ==

<mmtsbToolExample cmd="checkin.pl" set="/apps/mmtsb/bench/checkin.pl-test/test1"></mmtsbToolExample>

<mmtsbToolExample cmd="checkin.pl" set="/apps/mmtsb/bench/checkin.pl-test/test2"></mmtsbToolExample>

<mmtsbToolExample cmd="checkin.pl" set="/apps/mmtsb/bench/checkin.pl-test/test3"></mmtsbToolExample>

@@ Line 55: / Line 55: @@
 ; -help : usage information
 ; -sicho : checkin SICHO chain
-; -seq file :
+; -seq file : provide SICHO sequence file to rebuild all-atom structures from SICHO chain
 ; -at index : checkin at specific index in ensemble
 ; -dir datadir : data directory

@@ Line 54: / Line 54: @@
 ; -help : usage information
-; -sicho :
+; -sicho : checkin SICHO chain
 ; -seq file :
-; -at index :
+; -at index : checkin at specific index in ensemble
-; -dir datadir : checkin to specified directory
+; -dir datadir : data directory
-; -f filelist :
+; -f filelist : external file with list of files to be checked
-; -links :
+; -links : create symbolic links rather than coyping files
-; -verbose :
+; -verbose : write out information during checkin
-; -[no]compress : compress PDB structures using tgz
+; -[no]compress : (do not) compress PDB structures using gzip
 ; -dcd PDBtemplate CHARMMtrajectory : checkin structures from a trajectory file into an ensemble
 ; -dcdskip value : skip structures according to the given value

@@ Line 15: / Line 15: @@
 ([[enslatsim.pl]], [[ensmin.pl]]),
 or replica exchange sampling ([[latrex.pl]] and
-<docmark>aarex.pl</docmark>) this script is intended to
+[[aarex.pl]]) this script is intended to
 setup an ensemble data structure from structures generated elsewhere
 so that ensemble-based MMTSB tools can be used for structure evaluation

@@ Line 13: / Line 13: @@
 While a number of MMTSB tools directly generate ensembles from
 running multiple lattice simulations and all-atom refinement
-(<docmark>enslatsim.pl</docmark>, [ensmin.pl]),
+(<docmark>enslatsim.pl</docmark>, [[ensmin.pl]]),
-or replica exchange sampling ([latrex.pl] and
+or replica exchange sampling ([[latrex.pl]] and
 <docmark>aarex.pl</docmark>) this script is intended to
 setup an ensemble data structure from structures generated elsewhere

@@ Line 40: / Line 40: @@
 instead of PDB files. All-atom structures in PDB format are automatically
 rebuilt from SICHO chains if a MONSSTER sequence file is available
-(see: <docmark>genseq.pl</docmark>). If the name of the sequence file is
+(see: [[genseq.pl]]). If the name of the sequence file is
 not available from the ensemble configuration files it may by given
 with <B>-seq</B>.<BR><BR>

@@ Line 8: / Line 8: @@
 This script is used to add PDB files or SICHO chain files to
 an ensemble of protein structures.<BR>
 Ensembles are used in structure prediction to obtain statistically
 meaningful energy scores for structural families