3D Analysis :: Reduce Software for Adding Hydrogens
Reduce
Reduce is temporarily being distributed as two versions - Reduce3.1x and Reduce3.03 - due to the changes in PDB nomenclature. There is a new HET dictionary to be used with Reduce3.1x. The new version, Reduce3.1x, reads "old" (PDB version 2.3) and "new" (PDB version 3) PDB format files and writes "new" PDB format files by default. Reduce3.1x will write "old" PDB format files if the -OLD program flag is used AND one inputs an "old" PDB file AND the old HET dictionary is used (via the -DB flag).
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. (
PDF, 804KB)
Two tables list the current downloads for Reduce. The first table contains the new stuff. As noted above, there are now two HET dictionaries:
reduce_wwPDB_het_dict.txt uses PDB version 3 atom and residue nomenclature and is listed in the first table
reduce_het_dict.txt uses PDB version 2.3 atom and residue nomenclature and is listed in the second table.
| Platform | Version | Release date | Download size | Program (click to download) |
|---|---|---|---|---|
| Linux | 3.14 | 21-Aug-08 | 233 (Kb) | reduce.3.14.080821.linuxi386.gz |
| Mac OSX(2) universal binary |
3.14 | 21-Aug-08 | 459 (Kb) | reduce.3.14.080821.macosx.ub.zip |
| Windows | 3.14 | 21-Aug-08 | 4511 (Kb) | reduce.3.14.080821.win32.zip |
| Source code | 3.14 | 21-Aug-08 | 5077 (Kb) | reduce.3.14.080821.src.tgz |
| HET dict. | "new" | 31-Jul-07 | 2 (MB) | reduce_wwPDB_het_dict.txt.zip |
| Platform | Version | Release date | Download size | Program (click to download) |
|---|---|---|---|---|
| Linux i386 | 3.03 | 07-Mar-07 | 285 (Kb) | reduce.3.03.070307.linuxi386.gz |
| Linux x86_64 | 3.03 | 07-Mar-07 | 236 (Kb) | reduce.3.03.070307.linux.x86_64.gz |
| Windows | 3.03 | 07-Mar-07 | 146 (Kb) | reduce.3.03.070307.win.exe.zip |
| Mac OSX(1) | 3.03 | 07-Mar-07 | 209 (Kb) | reduce.3.03.070307.macosx.i386.zip |
| Mac OSX(1) | 3.03 | 07-Mar-07 | 400 (Kb) | reduce.3.03.070307.macosx.ppc.zip |
| SGI-irix | 3.03 | 07-Mar-07 | 697 (Kb) | reduce.3.03.070307.irix65.gz |
| Tru-64 | 3.03 | 07-Mar-07 | 1091 (Kb) | reduce.3.03.070307.tru64.gz |
| Source code | 3.03 | 20-Oct-06 | 1237 (Kb) | reduce.3.03.061020.src.tgz |
| HET dict. | "old" | 31-Jul-07 | 2 (MB) | reduce_het_dict.txt.zip |
If you encounter an error in downloading, try to get the file from our browsable download section.
(1)Reduce is run from the command prompt. (Start - Run - "cmd")
(2)Reduce is a unix program run from the command-line.