From: Axel Kohlmeyer (
Date: Thu Mar 27 2008 - 07:26:05 CDT

On Thu, 27 Mar 2008, Olaf Lenz wrote:

OL> > BTW, it may be convenient to include an -updatebonds (default off) flag
OL> > that will call 'mol bondsrecalc <mol>' after the (final) wrap.
OL> This would be just one part of the story, as it only works for all-atom
OL> systems that do not predefine bonds.

yes. but people who predefine bonds (i.e. everbody that does
bio-systems) are most likely to use -compound residue to wrap
water and then no bonds need to be recalculated

OL> For others, it would probably be nice to have a function that simply
OL> deletes all bonds above a certain length. Or maybe it would be better to

that can be a lot... i'm personally quite happy with the current
implementation. despite it being occasionally annoying, it also
indicates when there is a problem _and_ it is 100% deterministic.
if we try to make the representations smarter, we may end up with
more problems than what we are solving. KISS!

i'd rather see a more controllable implementation of dynamic bonds,
which is expected to be "slow".

OL> add a "maximal length" parameter to the bond-drawing representations, so
OL> that bonds longer than this maximal length are not drawn? What do you
OL> think of that?

too time consuming. the lines rep in VMD is very fast and can handle
very large systems. we should keep it at that.


OL> Best regards
OL> Olaf
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Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.