OK, Miguel and I agree:
connect hbonds auto (*) (*)
is the preferred exact replacement for
hbonds on
Upon review of a variety of systems, we find:
Rasmol 2.6 and Chime 2.6:
- hydrogen bonds present in PDB file CONECT are never displayed.
- "hbonds ON" only displays calculated hydrogen bonds
Jmol 10.00:
- hydrogen bonds present in PDB file CONECT are not displayed by default.
- "hbonds ON" adds to this set a set of calculated hydrogen bonds
and displays them along with the file-based hydrogen bonds.
- there is no way to display JUST the file-defined hydrogen bonds.
Jmol 10.1:
- hydrogen bonds present in PDB file CONECT record are displayed by default
- "connect hbonds auto (*) (*)" adds to this set a set of
calculated hydrogen bonds and displays them.
- "connect delete hbonds (*) (*)" deletes all hydrogen bonds
- "connect hbonds auto (*) (*)" after deletion shows
calculated bonds ONLY, not the file-derived set.
Thus, in Jmol 10.1 you will see a difference from previous versions of
Jmol and from Rasmol/Chime in that:
(a) Hydrogen bonds that are present in a CONECT record will now be
displayed by default. If you don't want them, use "hbonds off"
along with the load command.
(b) Calculated hydrogen bonds can be added using
connect hbonds auto (*) (*)
(c) Deletion of hydrogen bonds is without regard to their source --
file-based, Jmol-calculated, or user-defined. But we are considering
developing this in the future.
Bob and Miguel
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