[Chimera-users] H bonds

[Elaine Meng]

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 at 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

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