From: Axel Kohlmeyer (
Date: Fri Feb 09 2007 - 10:52:01 CST

On Thu, 8 Feb 2007 wrote:


MW> Hello
MW> I am having extreme difficulty doing what are seemingly the most basic
MW> things in VMD. For example, I have two PET molecules that I have moved to

not really. your basic mistake is that you see VMD as a 'molecule
editor', but in fact it is a visualization and analysis tool. when
working with VMD you always have to keep that in mind. also you
have to realize that the GUI is for most of the time is simply a
front-end for executing commands in the extended TCL intepreter
(or in more recent times also the python script engine) embedded
into the executable. so to understand what VMD really does, and
why it does not do what you assume it would do, you have to learn
a little bit about things that may be rather unrelated to what you
want to do. as other people already have stated, it will pay of
big time in the long run.

MW> major). Could someone please give me some pointers, outside of "read the
MW> tutorials?"

well, the major piece of advice is: never assume to know what the
programmer had intended to do when you use a feature of a program.
chances are, you'll go wrong. i've been down that road a few times,
even with packages that do the exact same thing, and even share a
common code base it can happen, that what appears to be the same
feature can have very different and puzzling consequences.

apart from that, going over the tutorials and 'playing' around will
provide you with the 'spirit of VMD' (if you can call it that) and
then at some point, you will it will suddenly it will start making
sense to you and become easy and you'll never understand why you
had these problems in the first place. the same is true for any
scientific/research work. the 10% of your time where it is easy is
the most important work you'll do, but the 90% of the time where
you are struggling to make sense of everything is required to be
able to get it done. remember you're preparing to work in a field
where - unlike in a test - the answers are not know a priori, but
_have_ to be induced from the evidence.

i guess most of the practical suggestions that were already made,
should have helped you to get some results by now.

good luck,

MW> Any help is sincerely and greatly appreciated.
MW> Thanks,
MW> Matt Wolfinbarger

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.