From: Axel Kohlmeyer (
Date: Sun Mar 07 2010 - 10:53:39 CST

On Sun, 2010-03-07 at 09:55 +0100, Francesco Pietra wrote:
> Hi:

dear francesco,

> New to trajectory_path.tcl, I dare placing a question. In my usage

please try to be more lucid. i needed to read
your mails three times to be able to have an
educated guess for what might have gone wrong.

i understand that it is difficult to describe
visuals, but in that case, a (small) screenshot
would have worked wonders (converted to jpg and
suitably scaled down it should be below the
mailing list size limits for attachments.)

> source trajectory_path.tcl
> set myligand [atomselect top "resid for.myligand"]

please check the "contents" of this selection!
does it only contain your ligand? could it be
that some other residues have the same residue id?
resid it the number that VMD reads from the file
and is by no means guaranteed to be unique. most
of the time, you have to combine this with selecting
the chain or the residue name or something else
that makes this unique.

> trajectory_path $myligand scale (which, grossly scales from red to
> yellow, cyan and finally blue)

if you don't like the color scale, why do you use the "scale" flag?

> there is a large shift in the coordinate scale between the path that

this "shift in coordinate scale" is a very strange expression.
i can only assume you mean that the path drawn by trajectory
path is displaced relative to the one you would expect.

> can be followed from VMD Main and that described with
> trajectory_path.tcl. Also, although the two are identical, the latter
> is on a much smaller scale. The shift is so large that the path

this part that is the most confusing. "identical", "shifted",
and "smaller scale" mean three different things to me. so it
is hard to imagine how it could be all three at the same time.

> described with trajectory_path.tcl is seen entirely at the immediate
> outside of the protein.

for cases like this, it is typically best to upload the files
and/or scripts to the VMD BioFS on biocore (just create a directory
under testfiles) and produce a (small) image. that would
take out a lot of the guesswork and make it easier to help.

we have been using trajectory_path.tcl in our comp. chem. classes
for years (that is where the latest modifications came from) and
it has been working fine for us and exactly as documented.


> thanks
> francesco pietra

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.