Hi Randy, Oh, H bonds, not H-bonds! I see what you mean. I am guessing it is because you have all the hydrogens in residue 1, whereas the CA that they are supposed to be attached to are in residue 0. However, simply changing everything to residue 1 causes trouble because what you have is not really ALA but some other thing with an extra methyl group. If you change the residue name to something nonstandard, say UNK, and residue 1, the structure is bonded as it should be when opened in Chimera. (file attached) If you don't do any file editing, however, you can add the bonds in Chimera by choosing Tools... Structure Editing... Build Structure and going to the Add/Delete Bonds tab. Then, select the 4 atoms and click the button to add all reasonable bonds. Best, 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