VMD-L Mailing List

From: maxim todoru (mtodoru_at_gmail.com)
Date: Fri Nov 12 2021 - 22:20:18 CST

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.
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 ?

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.
>
> On Sun, Nov 14, 2021 at 4:02 AM maxim todoru <mtodoru_at_gmail.com> wrote:
>
>> I just recalculated and new files have been generated.
>> https://urldefense.com/v3/__https://www.mediafire.com/file/8o1w2irxgb1h3yj/diazomethane_elf.cube/file__;!!DZ3fjg!pO1a2mwoObqfnugOl905FhBiBnJyYLBdQk0EmECmYcw3nt_EU99-aaFlQ8KVcshtqg$
>> https://urldefense.com/v3/__https://www.mediafire.com/file/t3sn5mc49lbefy9/diazomethane_syn.cube/file__;!!DZ3fjg!pO1a2mwoObqfnugOl905FhBiBnJyYLBdQk0EmECmYcw3nt_EU99-aaFlQ8IUWahLeA$
>>
>> Le dim. 14 nov. 2021 à 09:44, Axel Kohlmeyer <akohlmey_at_gmail.com> a
>> écrit :
>>
>>> Ok. But those two files don't match, so you cannot easily create a
>>> visualization from them.
>>> The data and atom positions in the second file have a different position
>>> and orientation than in the first.
>>>
>>> ```
>>> Cube File
>>> ELF grid
>>> 5 -5.050000 -6.850000 -8.100000
>>> 102 0.100000 0.000000 0.000000
>>> 138 0.000000 0.100000 0.000000
>>> 156 0.000000 0.000000 0.100000
>>> 6 6.000000 0.000000 0.000000 -2.153297
>>> 7 7.000000 0.000000 0.000000 2.441117
>>> 7 7.000000 0.000000 0.000000 0.292850
>>> 1 1.000000 0.000000 1.798526 -3.108993
>>> 1 1.000000 0.000000 -1.798526 -3.108993
>>> ```
>>>
>>> and
>>>
>>> ```
>>> ELF grid
>>> 5 -7.500000 -6.800000 -5.000000
>>> 157 0.100000 0.000000 0.000000
>>> 137 0.000000 0.100000 0.000000
>>> 101 0.000000 0.000000 0.100000
>>> 7 7.000000 -0.287104 0.000179 0.000320
>>> 7 7.000000 -2.452843 -0.000085 -0.000291
>>> 6 6.000000 2.156895 -0.000060 0.000645
>>> 1 1.000000 3.118963 -1.800493 -0.002035
>>> 1 1.000000 3.119299 1.800194 -0.002035
>>> ```
>>>
>>> On Sun, Nov 14, 2021 at 2:10 AM anas forum <anasforum05_at_gmail.com>
>>> wrote:
>>>
>>>> Dear Axel,
>>>> the whole process of visualization is explained in the attached image
>>>> Visualization_Process.jpg.
>>>>
>>>> https://urldefense.com/v3/__https://www.mediafire.com/file/tpj0gbhcj4te6c0/diazomethane_elf.cube/file__;!!DZ3fjg!pO1a2mwoObqfnugOl905FhBiBnJyYLBdQk0EmECmYcw3nt_EU99-aaFlQ8IMd93wJA$
>>>>
>>>> https://urldefense.com/v3/__https://www.mediafire.com/file/13h6ulencqwgzk8/diazomethane_syn.cube/file__;!!DZ3fjg!pO1a2mwoObqfnugOl905FhBiBnJyYLBdQk0EmECmYcw3nt_EU99-aaFlQ8JHTud05A$
>>>> About the color : red-cyan-green-purple
>>>>
>>>>
>>>> ᐧ
>>>>
>>>> Le dim. 14 nov. 2021 à 02:15, Axel Kohlmeyer <akohlmey_at_gmail.com> a
>>>> écrit :
>>>>
>>>>> I see no attachments in any of the e-mails in this thread.
>>>>> Also I would need a description of what volumetric data file you would
>>>>> want to use to represent the isosurface from and what other (volumetric)
>>>>> property/file you want to use for the coloring and more importantly, what
>>>>> the value (ranges) the different colors correspond to.
>>>>>
>>>>> On Sat, Nov 13, 2021 at 6:07 PM maxim todoru <mtodoru_at_gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Dear Axel,
>>>>>> Evidently, you did not understand the example that i posted, and more
>>>>>> probably you never face an example like that before, but i will explain the
>>>>>> situation again : i want to color one isosurface contain four domains with
>>>>>> four different colors, every color in the isosurface mean something.
>>>>>> if you have some time, i suggest you to give it a try, i uploaded the
>>>>>> necessary files before. Prove me if i'm wrong, because i'm pretty sure you
>>>>>> won't succeed get the desired results (attached image diaz.png).
>>>>>>
>>>>>> Best regards,
>>>>>> Maxim
>>>>>>
>>>>>> Le samedi 13 novembre 2021, Axel Kohlmeyer <akohlmey_at_gmail.com> a
>>>>>> écrit :
>>>>>>
>>>>>>> maxim,
>>>>>>>
>>>>>>> it looks like you did not pay sufficient attention to the
>>>>>>> suggestions that you have been given. While you cannot do the kind of
>>>>>>> custom color scale you desire through the GUI, it can very well be done
>>>>>>> from the script interface and that ability has been with VMD for a *very*
>>>>>>> long time.
>>>>>>>
>>>>>>> You need to use the `colorinfo` and the `color` command for that.
>>>>>>> The script to create custom matlab inspired color maps should be used as an
>>>>>>> instructive example.
>>>>>>>
>>>>>>> VMD maintains a list of "named" colors (`colorinfo num` will tell
>>>>>>> you how many) and then you have "indexed" colors up to a maximum (see
>>>>>>> `colorinfo max`).
>>>>>>> you can change either type of color with the `color change <index>
>>>>>>> <red> <green> <blue>` command. Where you provide the RGB values for a given
>>>>>>> index in the color map, first to the named colors then to the colors used
>>>>>>> for the color scale.
>>>>>>>
>>>>>>> I strongly suggest you and your "Tcl experts" have a second look at
>>>>>>> that script and the VMD user's guide.
>>>>>>>
>>>>>>> Axel.
>>>>>>>
>>>>>>> --
>>>>>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!pO1a2mwoObqfnugOl905FhBiBnJyYLBdQk0EmECmYcw3nt_EU99-aaFlQ8K_rCSiMA$
>>>>>>> <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!uTTRumpI9Guiwy96fYz-0HF61X21qAdlrRuK1erxmYs_2qfqpo8iCXvG20BntjwcFg$>
>>>>>>> College of Science & Technology, Temple University, Philadelphia PA,
>>>>>>> USA
>>>>>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!pO1a2mwoObqfnugOl905FhBiBnJyYLBdQk0EmECmYcw3nt_EU99-aaFlQ8K_rCSiMA$
>>>>> <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!uTTRumpI9Guiwy96fYz-0HF61X21qAdlrRuK1erxmYs_2qfqpo8iCXvG20BntjwcFg$>
>>>>> College of Science & Technology, Temple University, Philadelphia PA,
>>>>> USA
>>>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>>>
>>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!pO1a2mwoObqfnugOl905FhBiBnJyYLBdQk0EmECmYcw3nt_EU99-aaFlQ8K_rCSiMA$
>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>
>>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!pO1a2mwoObqfnugOl905FhBiBnJyYLBdQk0EmECmYcw3nt_EU99-aaFlQ8K_rCSiMA$
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>