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 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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