normal Bead Color

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2 years 5 days ago #5328 by cg-rookie
cg-rookie created the topic: Bead Color
Hello,

I have been working on parameterizing a new molecule but am having trouble visualizing the beads in vmd. The structure is made of 40 different beads with 4 different types of beads. When I load the structure into vmd the color scheme does not make sense. Does anyone know how to change/control the bead color in vmd?

Thank you!

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2 years 2 days ago - 2 years 2 days ago #5331 by Pim
Pim replied the topic: Bead Color
Hey,

You can find more info on visualisation here:
md.chem.rug.nl/index.php/tutorials-general-introduction/cgviz
md.chem.rug.nl/index.php/rb

It links to a script (cg_bonds.tcl) that you can run in vmd to autoset bonds and colors for martini systems.

It's a bit hard to define the best color for a bead, typically I adapt it manually per system I'm studying.
Last Edit: 2 years 2 days ago by Pim. Reason: clarification

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