From: John Stone (
Date: Tue Jun 09 2015 - 16:19:29 CDT

  Rather than hiding atoms by setting their colors to the background, you should
instead use VMD atom selections to select or hide the atoms. Most likely you ended
up with some overlapping duplicate copies of the same atoms, but with different colors,
and one of the cases with the default colors "won". If you use the VMD atom selection
fields correctly, you can prevent this from happening. If you haven't done so already,
now would be a good time to work through the VMD tutorials.

  John Stone

On Tue, Jun 02, 2015 at 08:34:19AM -0600, Xiaohui She wrote:
> Dear all,
> I changed the atom colors of the system through representations, and hid some atoms by setting the atoms the same color as the background, then output the image using "render-tachyon". The output image showed the default colors of the atoms, not the specified colors. Is there any method to solve this problem? I tried different render modes, and only the "render-snapshot" worked.
> Any suggestion will be appreciated.
> Best,
> Xiaohui
> University of Wisconsin-Madison

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