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Re: [Jmol-users] displaying colormap in jmol
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From: Kashi N. S. <kas...@gm...> - 2019-02-08 15:24:47
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Hi Otis, Thanks for this information. I will look into it. If you figure out a simpler way, please let me know. If I would be able to do here, then I will also let you know. Kashi On Fri, Feb 8, 2019 at 10:02 AM Otis Rothenberger <osr...@gm...> wrote: > Kashi, > > You may want to take a look at this: > > https://chemapps.stolaf.edu/jmol/docs/?ver=14.22#colorscheme > > I have to explore in more to see if it has any options for you. I've never > used it. Take a look. > > Otis > > > > On Fri, Feb 8, 2019 at 9:49 AM Kashi Nath Subedi <kas...@gm...> > wrote: > >> 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 >>>>> >>>>> _______________________________________________ >>>> Jmol-users mailing list >>>> Jmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>>> >>> -- >>> Otis Rothenberger >>> http://chemagic.org >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > -- > Otis Rothenberger > http://chemagic.org > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |
