[Chimera-users] Missing segment confuses addH

Sam Egel ssegel at purdue.edu
Wed Jun 12 20:47:57 PDT 2013


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,

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