Hi Dave, Just use the AddH tool or the command "addh" to add hydrogens to your structure: The residues are defined to give the most likely protonation states at physiological pH: lysine and arginine sidechains will be "protonated" (formal charge +1) and aspartic and glutamic acid sidechains will be "deprotonated" (formal charge -). Protonation states are mentioned in the AddH man page: http://www.cgl.ucsf.edu/chimera/1.2199/docs/ContributedSoftware/addh/ addh.html If you actually wanted the less common neutral states, it is easy for lysine and arginine: just select (Ctrl-click) the hydrogen(s) you want to delete and use Actions... Atoms/Bonds... delete (or the command "delete sel"). For aspartic and glutamic acids, you would need to force the program to add a hydrogen that it normally wouldn't, which can be done but involves a longer explanation. If you want that explanation, let me know. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 23, 2006, at 6:22 PM, Dave Roe wrote:
Is there functionality that will - add a hydrogen (if needed) to all Lysines and Arginines to give the protonated form - remove a hydrogen (if needed) from Aspartic and Glutamic acids to give the deprotonated form?
-- Dave Roe roex0050@umn.edu
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users