Package: reduce Version: 3.14.080821 Revision: 1 Maintainer: W. G. Scott Description: Adds hydrogens to a pdb file License: BSD GCC:4.0 HomePage: http://kinemage.biochem.duke.edu/software/reduce.php Source: http://kinemage.biochem.duke.edu/downloads/software/%n31/%n.%v.src.tgz Source-MD5: 0ac3ca9f592e3f4aa088a28a9ed89a18 Source2: http://kinemage.biochem.duke.edu/downloads/software/%n31/%n_wwPDB_het_dict.txt.zip Source2-MD5: 4dbe6a5a9a40af7c5835aa047556a807 Source3: http://kinemage.biochem.duke.edu/downloads/software/%n31/%n_het_dict.txt.zip Source3-MD5: 7a10e36dd9f3eb981510759ec2ab3413 DescDetail: << Reduce is a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed. HET groups can also be processed as long as the atom connectivity is provided. A slightly modified version of the connectivity table published by the PDB is available below. Note that the HET dictionary is available in two "flavors" - new and old (again). Which one to use is dependent upon which type of reduced PDB you want as output. The program is described in Word, et al.(1999) "Asparagine and glutamine: using hydrogen atom contacts in the choice of sidechain amide orientation" J. Mol. Biol. 285, 1735-1747. << PatchScript: << #!/bin/zsh -evf rm -f **/*.o rm -f **/*.a cd %n_src perl -pi -e 's|/usr/local/%n|%p/share/%n/%n|g' Makefile* SConscript << CompileScript: << #!/bin/bash -evf make clean make << InstallScript: << #!/bin/bash -evf mkdir -p %i/bin cp %n_src/%n %i/bin/. mkdir -p %i/share/%n cp ../%n_het_dict.txt %i/share/%n/. cp ../%n_wwPDB_het_dict.txt %i/share/%n/. << DocFiles: README.usingReduce.txt