Re: [modeller_usage] Hydrogen Atom Preservation

Alexander,

The program Reduce from the Richardson lab ( http://kinemage.biochem.duke.edu/software/reduce.php ) does a good job adding hydrogens to protein structures, and there are many other modeling programs that can perform that step (some listed here: http://kpwu.wordpress.com/2012/02/24/add-protons-hydrogens-to-structure/ ).

Although these programs will not solve your problem if you must *preserve* the locations of hydrogens in the structure you input to Modeller, that requirement is relatively uncommon.

Hope that helps, -J'n