Re: [Jmol-users] Manually colouring elements

[Brenton H. <bre...@ym...>]

Yep that is the goal, but this [1 <http://i.imgur.com/vOUQl2D.gif>] is 
the result I get from the capture command (CAPTURE "file.gif" 10 
transparent).

ps. is there any way I could attach my files to these emails without it 
having to go through the whole approval process by moderators? Because 
it's a pain having to upload them to Google Drive or imgur.

On 16/10/2014 5:03 AM, Robert Hanson wrote:
> I'm trying to figure out something -- is the end goal to make animated 
> GIFs or something else? Because now you just do that directly in Jmol, 
> right? No need for all the files or GIMP. Just use the CAPTURE command.
>
> Bob
>
> On Wed, Oct 15, 2014 at 12:58 PM, Rolf Huehne <rh...@fl... 
> <mailto:rh...@fl...>> wrote:
>
>     On 10/15/2014 05:59 PM, Brenton Horne wrote:
>
>         60 frames at 400x181 resolution: [1
>         <https://drive.google.com/file/d/0B1_sXH68hMWBMzBGa2ZJbDFPZTA/view?usp=sharing>]
>
>         60 frames at 1362x617 resolution: [2
>         <https://drive.google.com/file/d/0B1_sXH68hMWBc0tURDBWczJrNWM/view?usp=sharing>]
>
>         180 frames at 1362x617 resolution: [3
>         <https://drive.google.com/file/d/0B1_sXH68hMWBbVBFZ1FCdzFBdk0/view?usp=sharing>]
>
>         I don't even know how to do indexing.
>
>     I don't know what goes wrong on your computer. It looks much
>     better if I do it on my computer. See the file (temporarily)
>     available here:
>     http://www.fli-leibniz.de/~rhuehne/jmol/Bupropion-crystal_1362x617_180_frames.gif
>     <http://www.fli-leibniz.de/%7Erhuehne/jmol/Bupropion-crystal_1362x617_180_frames.gif>
>
>     There wasn't even much difference wheter I have set 'indexed' mode
>     manually or not. But I would still recommend doing it manually.
>     I tried to explain how to do indexing in one of my previous
>     answers on this thread.
>
>     In the GIMP menu select entry "Image", then subentry "Mode" and
>     then subentry "Indexed...".
>     This should open a dialog window. there you should select as
>     options "Generate optimum palette" with "Maximum number of colors
>     255" (1 color is needed for transparency) and for "Color
>     dithering" one of the two "Floyd-Steinberg" options.
>
>     Since the major part of your structure is black it doesn't seem to
>     be a very good idea to choose almost black as the transient
>     background color during image generation. So I added another
>     parameter 'transientBackgroundColor' after the 'stepCommandSet'
>     parameter to the new version of the function in the attached file.
>     "yellow" might work better in your example.
>
>     As you might see in my GIF file, there are still some remaining
>     black pixels from the background, For example around the atoms.
>
>     You might try to run the command 'setAntialiasImages off' before
>     running the 'exportAnimation' command.
>
>     Which version of GIMP do you use on which platform? Maybe this
>     could explain why your result is much worse.
>
>
>     Regards,
>     Rolf
>
>
>
>
>     -- 
>
>     Rolf Huehne
>     Postdoc
>
>     Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
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>
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>
> -- 
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
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