Important note to all users: Implications of proposed Version 10.1
change re hydrogen bonds.
The current prerelease of 10.1 includes a major improvement in the way
bonds can be created, modified, and deleted. It is the "connect"
command. Miguel has created an amazingly powerful command here and
introduced totally revolutionary functionality into Jmol with it. Mostly
this is all new functionality, but there is one implication everyone who
works with proteins needs to know. It is this:
hbonds on
will appear "broken" if you just replace 10.00 jar files with the
proposed 10.1 jar files.
Instead, you will need to use:
connect hbonds auto (oxygen) (nitrogen)
The quick question is: *How much of a problem will this be for you?*
Advantages of the new method of displaying hbonds include:
-connect hbonds auto is more efficient and selective than the old
"hbonds on". You can specify *which* oxygens and nitrogens you want
connected -- (oxygen and 1-12) for example.
-connect hbonds auto (oxygen) (nitrogen) allows for future development
when there may be additional schemes for calculating hydrogen bonds.
-connect hbonds auto (oxygen) (nitrogen) needs to be only given once per
file load, but it can certainly be given multiple times. That is, one
could just replace all occurances of "hbonds on" with "connect hbonds
auto (oxygen) (nitrogen)" with probably no observable effect.
-once this command has been given, hbonds can be turned off and then
back on using the hbonds command.
Bob
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