Miguel wrote:
I would assume that people *would* want them to be the same diameter.
I'd be quite surprised if this is true. Hydrogen bonds are a much more
subtle sort of bonding, deserving the current thin dotted line I see here.
If you think that they should be mad==1 then I guess that is OK.
That would be my preference.
But they should have the same size as hbonds when they are embedded in the
molecular model file.
OK, I checked this out --
the default is "hbonds OFF"; even CONECT hydrogen bonds are not
displayed until an "hbonds ON" command is issued. Basically, the bonds
are created with mad=0, but "hbonds ON" sets them to the default mad=1.
I think we should change this default to be "hbonds 1". Note that
without this modification, there doesn't appear to be an option to
render only the hydrogen bonds indicated in the PDB file. Current
rendering of hydrogen bonds requires adding in Jmol-calculated hydrogen
bonds.
Interestingly, when I load my test file with Raswin, what I get is (a)
default hbonds OFF; (b) no CONECT or HYDBND hbond shown -- only the
calculated ones -- ever, even with "hbonds ON".
Bob
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