Changing default parameters

If you are using certain commands and change default parameters frequently, you can add a line in your ~/.mgltools/1.4.5/Pmv/_pmvrc to change these values. To find the syntax of a command, run the command you are interested in, and click on the Message Box icon on the ToolBar. Here are a couple of examples.

Make Color by Atom Type the Default

When reading a molecule, PMV displays white lines between bonded atoms. If you like these lines colored by atom type instead, append the following line to _pmvrc:

self.setOnAddObjectCommands(['buildBondsByDistance', 'displayLines', 'colorByAtomType'], log=0)

Change Default Ball Radii

To change ball radii in display sticks and balls, run Display → Sticks And Balls, change Ball Radii from 0.3 to, e.g., 0.5 and click OK. Check the Message Box to see the command log. There should be a line somewhat similar to the following:

self.displaySticksAndBalls("HIS", log=0, cquality=0, sticksBallsLicorice='Sticks and Balls', bquality=0, cradius=0.2, only=False, bRad=0.3, negate=False, bScale=0.0)

This shows the command that has been executed self.displaySticksAndBalls and corresponding arguments. The one we are interested is bRad. Now edit ~/.mgltools/14.5/Pmv/_pmvrc and append the following line to the end:

self.displaySticksAndBalls.lastUsedValues['default']['bRad'] = 0.5

Display Sticks and Balls Colored by Atom Type

Q: If you change the display from lines to sticks and balls, the molecule becomes colorless even if you already colored the lines by atom type. Is there a way to keep the color scheme?

A: Append the following code to _pmvrc:

self.setOnAddObjectCommands(['buildBondsByDistance','displayLines','displaySticksAndBalls','colorByAtomType','undisplaySticksAndBalls'],log=0)