From: Axel Kohlmeyer (
Date: Thu Sep 13 2012 - 04:18:16 CDT

On Thu, Sep 13, 2012 at 10:12 AM, BIO MED <> wrote:
> hello!
> after loading a protein, I get this:
>>Main< (initial) 1 % listall()
> invalid command name "listall()"
> why?

why not?

> how do I generate a full report of the molecule I have loaded?
> list of all atoms
> numbers of each atom
> positions of each atom
> each bond
> numbers of each bond
> etc

this is all documented in the user's guide.

> thanks!
> PS1: I found what is problematic imo with the tutorial: you cannot read it
> in parts, you have to go through it from the begining. It should have
> hyperlinks of terms in each page, pointing to their reference, so that a
> reader would read a page in the middle of the tutorial and be able to
> understand everything (after visiting the hyperlinks of the terms he doesnt
> know).

if you know how to do this, please go ahead and do so.
this is a

> PS2: Btw, what's the whole point of having both tutorials and manuals? I
> mean, come on, just make a well organized file and let it be single!

that is because there is a big difference between a tutorial (which
will teach you a process) and a user's guide (which documents features).
most user's guide also contain generic tutorial segments, but those
are not as focused as most tutorials are and usually separate from
the reference sections.

it looks what you need is a personal consultant with lots of VMD
experience. if you make an attractive offer, perhaps somebody will
volunteer to spoon feed you the information you want in the digested
style that you are looking for.

short of that, i would say that you are stuck with having
to learn things step by step, like everybody else did, and
live with the risk that you may be learning more (useful)
things in the process than what you think you need right now.

c'est la vie, especially for no-cost software.


Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.