From: Miguel <mi...@jm...> - 2006-04-05 19:36:34
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> Thank you, Miguel. Right, there are many ways to do this. This note is > intended specifically for those users who already have =22hbonds on=22 > built into their pages that involve links or buttons. The key point is > to make sure you do not use just > > connect hbonds auto; > > in your scripts as a replacement for =22hbonds on=22, as those are not > equivalent, Correct. In RasMol/Chime/Jmol 10.00 the 'hbonds on' command was not dependent upon= the selection set. > and that you check your pages for instances of =22hbonds on=22 > prior to installing Jmol version 10.1. In this context, > > connect hbonds auto (*) (*) > > or > > connect hbonds auto (nitrogen) (all) > > are precise replacements for =22hbonds on=22 in this context. Be advised that there *is* another twist to this to this story. I tried t= o point it out in my email notification, but it may not be clear to all. In RasMol/Chime/Jmol 10.0, the behavior of 'hbonds on' depends upon whether or not there are author-defined hbonds in the underlying file. Therefore, it is not the case that 'connect auto hbonds (*) (*)' is a direct replacement for 'hbonds on' IF you have files which contain hbonds within the files AND you blindly replace your 'hbonds on' -> 'connect auto hbonds (*) (*)' THEN you will change the behavior because you previously did not have calculated-hbonds= but now you do. Miguel |