Actually, upon closer look, the
residue wasn't defined using the proscribed PDB alternate location identifiers,
so in fact, PyMOL itself is unable to avoid misconnecting the
Thus, you'll need to use "unbond"
set connect_mode = 0 is the default, and this uses
both distance-based and explicit (CONECT-based)
connect_mode = 1 uses only explicity
we don't have a connect_mode = 2 yet
(forcing use of distance-based connectivity only), so instead, you'll need to
remove the errant CONECT records from the "new & improved" pdb file or
simple unbond the mis-connected
This was previously discussed in an archived email but I can't
find it right now. Does the setting connect_mode=0 use the CONECT records in
the PDB file or not? I think it does. Apparently in pdb code 1ABE, the
CONECT records were changed in a 2005 revision. Two alternate sugar
conformations are now interconnected when using the current 1ABE. The old
1ABE (from 1993) seems fine.
Should setting connect_mode to 0 before loading PDB fix it? I don't
think it does.