VMD-L Mailing List

From: maxim todoru (mtodoru_at_gmail.com)
Date: Sat Nov 13 2021 - 03:30:11 CST

Dear Pr. Axel,
I'm truly sorry for my mistakes and bad behavior, and I deeply apologize to
you and Professor John Stone for not taking his advice more carefully, and
like you said before I should make more effort.
Thank you very much for your help, precious time and advice.

Best regards,
Maxim

Le dim. 14 nov. 2021 à 15:47, Axel Kohlmeyer <akohlmey_at_gmail.com> a écrit :

>
>
> On Sun, Nov 14, 2021 at 5:39 AM maxim todoru <mtodoru_at_gmail.com> 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.
>
> Axel.
>
>
>>
>> Le dim. 14 nov. 2021 à 10:59, Axel Kohlmeyer <akohlmey_at_gmail.com> 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 akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!rwV5dpV_bIl_fbjg1gLGnoHGEORnyUI0PxTfx4EQNjLrNvwapFJWxCwigt9QpWGTVw$
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>