VMD-L Mailing List

From: Olaf Lenz (olenz_at_fias.uni-frankfurt.de)
Date: Thu Mar 27 2008 - 06:33:42 CDT

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Hi!

Axel Kohlmeyer wrote:
>> So, what do you, i.e. the other users and developers of pbctools, think
>> of changing the default?
>
> whatever choice you make, there will always be people that find this unexpected.
>
> just think about all the "bio-people" that will have their water
> molecules "chopped"
> when you make -nocompound the default (and complain about it).
>
> it is the privilege of the maintainer of a package to choose.

*smile*
If it is my privilege, I will choose "-nocompound".

In fact, I think that this will generate the fewest questions, because
then at least "pbc wrap" does the most obvious thing, which is wrapping
all atoms. If it doesn't, people are rightfully confused. This is what
happened several times.

People that want certain compounds kept together will probably be
annoyed, but hopefully some of them will RTFM to see that it can keep
compounds together. Still, this is going to generate quastions, I'm
aware of that.

> BTW, it may be convenient to include an -updatebonds (default off) flag
> that will call 'mol bondsrecalc <mol>' after the (final) wrap.

This would be just one part of the story, as it only works for all-atom
systems that do not predefine bonds.
For others, it would probably be nice to have a function that simply
deletes all bonds above a certain length. Or maybe it would be better to
add a "maximal length" parameter to the bond-drawing representations, so
that bonds longer than this maximal length are not drawn? What do you
think of that?

Best regards
        Olaf
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