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Coloring by atom type

Adding missing hydrogens.


This tutorial introduces PMV and demonstrates its basic features. Note, this tutorial applies to version 1.4.3. There have been quite a few changes in PMV since version 1.4.3.
Page 3 of 7.
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 Colorby 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 FilePreferencesSet 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.
Since hydrogens are difficult to resolve with X-ray, we are going to add them using EditHydrogensAdd. This brings up the widget shown below.
Click OK to add missing hydrogens.
by Sargis Dallakyan last modified 2007-09-07 13:51
Contributors: Ruth Huey, Michel Sanner
Molecular Graphics Laboratory, TSRI

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