The Molecular Graphics Laboratory Forum

Hi there,

I am using MGL Tools v. 1.4.3 on Linux Cent OS.

Could someone please advice me if there is any way at all to change the background colour in the PMV ?

I can see how this can be done in the later versions; unfortunately though, 1.4.3 is the only one I was able to successfully run on our linux machine.

Thank you so much !

Coloring by atom type
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Adding missing hydrogens.

To gain a better understanding on the chemical structure of the molecule that we read, lets color this molecule by atom type.
To that end, click on Color → by Atom Type, check the Checkbutton next to lines and press OK. This colors our molecule using the following palette:

Hydrogens (H) - cyan
Carbons (C) - gray
Nitrogens (N) - blue
Oxygens (O) - red
Sulfurs (S) - yellow
Phospors (P) - magenta
All others - green

You could change PMV preferences so that all new molecules are colored by atom type. This is done by using File → Preferences → Set Commands to be Applied on Objects, which brings "Cmds called after adding an object" widget. Scroll down the list of "Available commands" and append colorByAtomType to "Commands to be applied" list.

If you need any additional information, I found this information here:

http://mgltools.scripps.edu/documentati ... -atom-type

Hope this helps.

JB