Tool Set Documentation

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usage: [options] tag [file(s)]
options: [-sicho] [-seq file]
         [-at index]
         [-dir datadir]
         [-f filelist]
         [-dcd PDBtemplate CHARMMtrajectory]
         [-dcdskip value]

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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 While a number of MMTSB tools directly generate ensembles from running multiple lattice simulations and all-atom refinement (,, or replica exchange sampling ( and 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. 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: 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.


usage information
checkin SICHO chain
-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
-f filelist 
external file with list of files to be checked
create symbolic links rather than coyping files
write out information during checkin
(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

Examples sample 1vii.sample.?.pdb
checks the structures from the files matching 1vii.sample.?.pdb into an ensemble in the current directory under the tag sample -dir data -f file.list sample
checks the structures from the files given in file.list into an ensemble in the data directory under the tag sample -at 5 sample 1vii.sample.1?.pdb
checks the structures from the files matching 1vii.sample.1?.pdb into an existing ensemble in the current directory under the tag sample beginning at index 5. Exisiting conformations at index 5 or higher are overwritten with the new ones.