Reduce adds hydrogens to HETATMs according to its "hetdict", which is a text file in the PDB Format for the chemical component dictionaries. A dictionary file is available for download from the url that you cited. Reduce will find the hetdict from either it's compiled path location, the location given by the environmental variable "REDUCE_HET_DICT", or the location given in the program flag "DB". Type 'reduce -help' for details. ... Or, you can use molprobity <http://molprobity.biochem.duke.edu/> to have reduce place hydrogens on your uploaded coordinate file.
On Sun, Jun 22, 2008 at 12:00 AM, U Sam <[EMAIL PROTECTED]> wrote: > If anybody have used "reduce" ( > http://kinemage.biochem.duke.edu/software/reduce.php) to fix hydrogens to > residues in PDB, then I highly appeciate suggestion on my problem as > follows. > Running "reduce" (new version 3.13) I can see hydrogens are fixed to > protein residues. > But if ligand is covalently or non-covantly bound to protein, then how > hydrogen is fixed to protein residue covalently bound to ligand or > noncovalent ligand using "reduce". I did not get any result on HETATM in the > PDB running "reduce" in the same way. > Thanks. Sam. -- Bryan Arendall Richardson Lab - Duke University kinemage.biochem.duke.edu 919-681-8827
