Re: [Jmol-users] displaying colormap in jmol

[Kashi N. S. <kas...@gm...>]

HI Otis,
Yeah its good to visualize that way for few linear chain atoms like that
but if you want to visualize the atoms in the amorphous materials for eg
you have 40 oxygen randomly distributed (of course separated by atleast
minimum distance), then using labels on each atom makes the visualization
complicated and you lost the meaning of color coding the atoms according to
the partial charge. So, visualization will be pretty neat if we have a
colormap on sides( usually kept on right of your image) with color pattern
changing with charge. If there is a way, please let me know.
Thanks,
Kashi

On Thu, Feb 7, 2019 at 9:55 AM Otis Rothenberger <osr...@gm...> wrote:

> Hi Kashi,
>
> I think George's solution is pretty neat! You could append his "model" in
> a line any place in your model window. It could colored, and it could show
> charge number labels. You would simply be making a line chart with H atoms.
> George, I love it!
>
> Otis
>
> On Thu, Feb 7, 2019 at 9:11 AM Kashi Nath Subedi <kas...@gm...>
> wrote:
>
>> Hi George,
>> Thanks for the information.
>> I am actually looking for the color map that has been used in displaying
>> on atoms. For example atom1 has charge -1 and has red color and atom 2 has
>> charge 1 and has blue color. Now, I want the picture to be self explained
>> by showing these colors outside the box as a colormap that represents
>> charge from -1 to 1 ie from red,.... blue
>> Thanks,
>> Kashi
>>
>> On Thu, Feb 7, 2019 at 8:58 AM lisensky <lis...@be...> wrote:
>>
>>> I have done something like this by displaying this model with labels.
>>> Example at https://chem.beloit.edu/Warming/pages/structures.html
>>>
>>>
>>> H7
>>> Jmol version 14.2.2_2014.06.29  2014-06-28 18:17 EXTRACT: ({0:9})
>>>
>>>   7  0  0  0  0  0              1 V2000
>>>   -4.50000   0.00000   0.00000 H   0  0  0  0  0  0
>>>   -3.00000   0.00000   0.00000 H   0  0  0  0  0  0
>>>   -1.50000   0.00000   0.00000 H   0  0  0  0  0  0
>>>    0.00000   0.00000   0.00000 H   0  0  0  0  0  0
>>>    1.50000   0.00000   0.00000 H   0  0  0  0  0  0
>>>    3.00000   0.00000   0.00000 H   0  0  0  0  0  0
>>>    4.50000   0.00000   0.00000 H   0  0  0  0  0  0
>>> M  END
>>> > <JMOL_PARTIAL_CHARGES>
>>> 7
>>> 1 -0.1
>>> 2 -0.05
>>> 3 -0.025
>>> 4  0.0
>>> 5  0.025
>>> 6  0.05
>>> 7  0.1
>>> $$$$
>>>
>>>
>>> George Lisensky
>>>
>>>
>>> On 2/7/19 6:32 AM, Kashi Nath Subedi wrote:
>>>
>>> Hi
>>> I have color coded atoms in a box according to the charge on them using
>>> 'color partialcharge'. I want to have the colormap displayed by the side of
>>> the simulation box (color gradiant) but I am unable to do so in jmol. I
>>> would appreciate for the help.
>>> Thank you
>>>
>>>
>>> _______________________________________________
>>> Jmol-users mailing lis...@li...://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>> --
>>> George Lisensky                 lis...@be...
>>> Chemistry Department            608-363-2225
>>> Beloit College                  fax 608-363-2052
>>> 700 College Street
>>> Beloit, WI 53511
>>> http://chemistry.beloit.edu/classes/lisensky
>>>
>>> _______________________________________________
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> --
> Otis Rothenberger
> http://chemagic.org
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