[Chimera-users] Transparency of surface colored with electrostatic potential file

Sarah Piper s.piper at imb.uq.edu.au
Tue Jan 17 16:17:17 PST 2017

Thanks Elaine
this helped a lot!


On 18 Jan 2017, at 4:04 am, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

Hi Sarah,
Sure, you can just use transparent colors for coloring the surface by electrostatic potential (ESP).  It sounds like you tried to first color by ESP and then make the surface transparent, which (as you saw) would not work.

Just open the structure, show the surface, and then open the ESP file.  I believe opening the ESP file will automatically start the “Surface Color” tool, but if it doesn’t, you can start that tool with menu: Tools… Surface/Binding Analysis… Electrostatic Surface Coloring.

In that tool, choose to color the molecular surface model according to the ESP, and then click each of the color wells to bring up the Color Editor.   In the Color Editor, there are bars for the R (red) G (green) B (blue) and A (opacity) components.  Click to use A < 1, say 0.5 for half transparent.  You would need to do this for each color.  Then your Surface Color dialog will look something like the image I attached, where the color wells show a diagonal indicating that the colors are transparent.  Then you can just click the Color button on the bottom to apply the coloring.  Of course, you could change the colors too, but red-white-blue is traditional for ESP coloring.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


On Jan 16, 2017, at 5:01 PM, Sarah Piper <s.piper at imb.uq.edu.au<mailto:s.piper at imb.uq.edu.au>> wrote:

I was wondering if you can make a surface transparent, which contains an electrostatic potential file (.dx), calculated with APBS? It would be nice to be able to see the ribbon structure of my .pdb file within the coloured surface.

I’m using mol maps or SES to create the surface (my surface calculations (MSMS) usually fails, probably because of too large .pdb files) and then color this surface (Surface Color) with the submitted potential file from APBS.

If I then want to make the surface with the potential colouring transparent, it doesn’t work. It just works to make the ’normal’ surface color itself transparent (e.g. transp 70,s #1).

Does anyone have an idea if I can make the potential file or surface with electrostatic potential transparent as well?

Many thanks for your help.
Best regards,

Sarah Piper, PhD student
Landsberg/King labs, Institute for Molecular Bioscience
University of Queensland, St Lucia, 4072 QLD, Australia

Phone: +61 7 3346 2325
Email: sarah.piper at uq.edu.au<mailto:sarah.piper at uq.edu.au>

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