[Chimera-users] H bonds

[Eric Pettersen]

Hi Randy,
	The disconnected hydrogens (H1, H2, H6) look like they should be  
bonded to the CA in residue 0.  The problem is that the hydrogens are  
in residue 1 and Chimera will never form cross-residue bonds that  
involve hydrogen unless there are explicit connect records.  Your  
options to fix this are:

	1) add CONECT records
	2) put those hydrogens in residue 0 and reorder the PDB file
	3) put all the atoms in residue 1 and give the CAs unique names.  I  
recommend changing the residue name to something other than ALA in  
this case.

As a footnote for option 3, you don't actually _have_ to give the CAs  
unique names.  You could still distinguish them in commands by serial  
number, e.g. color red @/serialNumber=1.  It's just a whole lot  
easier to give them unique names.  :-)

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

On May 27, 2008, at 10:56 AM, Randy Heiland wrote:

> I have a naive question - given the following pdb file:
>
> ATOM      1  CA  ALA     0       1.125   1.534   0.000  0.00
> 0.00      0    C
> ATOM      2  C   ALA     0       0.000   0.514   0.000  0.00
> 0.00      0    C
> ATOM      3  O   ALA     0      -1.173   0.853   0.000  0.00
> 0.00      0    O
> ATOM      4  N   ALA     1       0.394  -0.796   0.000  0.00
> 0.00      0    N
> ATOM      5  CA  ALA     1      -0.546  -1.905   0.000  0.00
> 0.00      0    C
> ATOM      6  H1  ALA     1       1.017   2.171   0.880  0.00
> 0.00      0    H
> ATOM      7  H2  ALA     1       1.017   2.171  -0.880  0.00
> 0.00      0    H
> ATOM      8  H3  ALA     1       1.381  -0.999   0.000  0.00
> 0.00      0    H
> ATOM      9  H4  ALA     1      -1.551  -1.486   0.000  0.00
> 0.00      0    H
> ATOM     10  H5  ALA     1      -0.420  -2.528  -0.890  0.00
> 0.00      0    H
> ATOM     11  H6  ALA     1       2.123   1.091   0.000  0.00
> 0.00      0    H
> ATOM     12  H7  ALA     1      -0.420  -2.528   0.890  0.00
> 0.00      0    H
>
> when I display it in Chimera, there are 3 unbonded hydrogens - why is
> that and is there a menu item to create/display the bonds?
>
> thanks, Randy
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