Tool Set Documentation

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Revision as of 14:31, 12 August 2006


usage: [options] intag outtag
options: [-dir workdir]
         [-run [from:]to]
         [-opt file[:file]]
         [-l min:max[=min:max=...]]
         [-hard value[:force]]
         [-soft value[:force]]

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This script is used to cut out parts of a protein in ensemble structures for loop or fragment modeling where it may be sufficient to consider only the surrounding local protein environment. It shares some of the options and functionality with <docmark></docmark> but in addition automatically considers all ensemble structures and generates a new set of reduced structures.
Required parameters are input and output tags and the definition of the loop or fragment residues with -l unless the fragment residues have been previously stored in the ensemble configuration file. Options may be used to provide the ensemble directory with -dir and select a subset of available structures with -run. The -hard and -soft options are equivalent to the same options in <docmark></docmark>.
The resulting restraint definition to be used in subsequent simulation or minimization runs is written to the options file of the output tag which may be read in later, e.g. by <docmark></docmark> using the -opt parameter.


usage information

Examples -dir data -l 34:41 -hard 14:5.0 -soft 10:1.0 whole lim
cuts out a protein fragment around the loop at residues 34 through 41 from all ensemble structures associated with the whole tag. The resulting PDB structure is stored under the tag lim. The residue cutoff is set to 14 A, a soft cutoff of 10 A is set to determine the residues for which weaker restraints are applied. The force constants for the restraints are set to 5 and 1 kcal/mol, respectively. The restraint definition is stored in the ensemble options file for subsequent minimization or simulation runs.