[Chimera-users] Missing segment confuses addH

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 13 10:38:10 PDT 2013

Hi Sam,
The problem is that Chimera is "smart" enough to realize that because there is a missing segment, those are not real termini.  If you want them recognized as real termini, probably the easiest way is to text-edit the PDB file to add a TER line where you want the chain to terminate.

Is it necessary to chop up your protein by writing only the active site residues to a file?  You could just save a session with only that part displayed.  I understand, however, that sometimes people need to do this for subsequent calculations.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 12, 2013, at 8:47 PM, Sam Egel <ssegel at purdue.edu> wrote:

> Hi,
> Basic Problem: I am attempting to use the addH tool on a metal containing active site I have extracted. The problem is that Chimera draws an 11 angstrom pseudo bond representing a missing segment between two residues. This bond seems to be the reason that a terminal carbon is receiving only two hydrogens rather than three. The pseudo bond runs right through the bond axis between two other carbons, both of which are protonated correctly. Can anyone please explain how to actually delete this bond (hiding through ~longbond, closing or hiding through the pseudo bond panel does not work) or provide another method to get this carbon to have three protons? I'm running v 1.6.2 of Chimera locally on Win 7 and the same problem occurs on a remote Red Hat Enterprise Linux machine running v 1.5 of Chimera.
> More Detail: Getting this carbon protonated in a one-stop-shop by Chimera would save me the world of time for a number of reasons, including that I need to make many files of this active site and every pdb of this enzyme has the same addH/pseudo bond problem between the same residues. The active site was extracted by writing a 10 angstrom zone around the metal to a pdb and then hand selecting the residues I cared about from there and writing them to a pdb. 
> Workarounds: I have tried using command line ~longbond, hiding and closing out the missing segments option in the pseudo bonds panel, and deleting the bond by highlighting it and trying to delete bond under the adjust bond tab in modify structure window. If I write the pdb to an xyz (Molden) and open the xyz in Chimera, addH works just fine. However, I would really like for these files to be real pdbs that have associated residue names at the moment (residue names are, of course, deleted when converted to xyz).
> Thank you for your time,
> Sam

More information about the Chimera-users mailing list