Bob Hanson wrote:
OK, Miguel and I agree:
connect hbonds auto (*) (*)
is the preferred exact replacement for
hbonds on
me, too, I consider the restriction on backbone hbonds calculation in
RasMol as a disadvantage which should be overcome in future connect
hbonds auto commands.
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.
they are displayed on load with RasMol 2.7
where further hbond calculation is suppressed, because there are already
hbonds
- "hbonds ON" only displays calculated hydrogen bonds
hbonds 50
displays all present (or calculated) hbonds in RasMol 2.7
...
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
is substituted to "connect create hbonds auto (*) (*)"?
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.
I agree, but what does
connect modify hbonds auto (*) (*)
with existing (CONECT record or connect min max create hbond (selection)
(selection) hbonds)?
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.
I don't think that this is necessary.
Regards, Jan
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