From: Axel Kohlmeyer (
Date: Sun Nov 14 2021 - 08:46:55 CST

On Sun, Nov 14, 2021 at 5:39 AM maxim todoru <> wrote:

> Dear Axel,
> I don't know what to say, but I have to express my sincere apologies, I
> was totally wrong, I am very sorry.

Yeah, it took me less than an hour to do something you were confident that
it cannot be done. ... and it would have been even less, if I had hardcoded
the colors and not made the function a bit more fancy by looking up the RGB
values of named colors. I was a bit surprised how quick this went by
myself, since I haven't done a visualization of a cube file in a couple of
years and I don't even remember when the last time was, that I was playing
around with colors from the command line. It must have been more than 10
years ago.

there are two important lessons to be learned here:

- it is very risky to judge what people know or don't know from e-mails. It
takes a whole lot of experience to read between the lines and to have seen
many similar questions about similar problems before you can make a
qualified guess. ... and from personal experience I can tell you that you
still get it wrong sometimes regardless how much experience you have.

- when people with some experience make some suggestions (and everybody
responding in this thread has significant experience with VMD, just google
their names and search their answers in the mailing list), you should make
a serious effort to re-evaluate your position *from scratch* and give the
advice given a more careful look. Regardless of well you think you have
covered everything and there is nothing left to explore, humans have a
tendency to overestimate their own skills and disregard those of others, if
things are not presented in exactly the way they expect it. ... and again,
from personal experience I can add that there is *always* something new to
learn and a different perspective can give new insights. So you'll find
that experienced people will not as easily dismiss something, even if they
would be correct to do so 99 out of 100 times.

> Could please explain the meaning of this line : "molinfo top set
> {center_matrix rotate_matrix scale_matrix global_matrix} {{{1 0 0
> -0.598522} {0 1 0 2.81096e-05} {0 0 1 0.000359421} {0 0 0 1}} {{-0.97148
> -0.235749 -0.0252959 0} {0.0394376 -0.265863 0.963197 0} {-0.2338 0.934732
> 0.26758 0} {0 0 0 1}} {{0.732539 0 0 0} {0 0.732539 0 0} {0 0 0.732539 0}
> {0 0 0 1}} {{1 0 0 -0.29} {0 1 0 0.08} {0 0 1 0} {0 0 0 1}}}" and on what
> basis you choose those values ?

These numbers represent the "viewpoint" of the specific visualization. The
specific meaning of the settings is explained in the user's guide. I didn't
choose those values, I copied them from a saved state file. You don't
really need them, but without them the visualization needs to be
repositioned and scaled and oriented to match the reference image. When
posting on a mailing list, I prefer not to post a complete saved state
file, but rather only the parts that are relevant to the given case and
different to the default settings, so that all other customizations a
particular person uses, remain intact and vice versa, you won't get my
personal customizations included.


> Le dim. 14 nov. 2021 à 10:59, Axel Kohlmeyer <> a
> écrit :
>> here you go.
>> attached is a visualization state that assumes the two cube files in the
>> current directory.
>> you can load it into VMD and it should produce the desired coloring as in
>> the attached image.
>> the custom color scale generation for a sequence of colors assuming an
>> assignment with consecutive values as in the syn file is at the end of the
>> file.
>> you can change the assigned colors any time with additional calls to the
>> "make_custom_colorscale" function.
>> axel.

Dr. Axel Kohlmeyer;!!DZ3fjg!ryleiYpDH531lRJpTaPKqjiV4ubITRIWq1uybuH2b7AsSs0uLd2BjvbUr1VsTy7bKQ$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.