Create Bonds On The Fly

Say you load a pdb file and discover (to your dismay) that the heme's iron is not bond to the surrounding carbons. Here's how to add bonds between the atoms (to make it proper).

1. Click Picking Commands. It's the hand pointing to the upper left.

2. Choose 'addBondsGC' from the first drop-down menu that appears.

3. Click the unbound atom, a yellow ball should appear upon it along with a label.

4. Click the atom to which you think it should be bound. A line will be drawn betwixt the atoms.

5. Repeat until proper affect achieved.

note: if you would like to keep these changes, be sure to save the molecule with the connect records as well as the 'UserDefined' bond types:

Fwd: Subcribe

If you would like to subscribe to this blog, please either post your email or send it to huntoon@scripps.edu, and I will sign you up, so you can get tips as soon as they are posted.

Jon Huntoon
Molecular Graphics Lab
The Scripps Research Institute

Color Map Tip

To make nice, straight lines for your color map, hold down the command/control key while you click and drag upon the color field. ;)

Adpative Poisson-Boltzmann Solver, APBS, continuum electrostatics

Need some electrostatics? Easy.

1. Load Molecule.

2. Goto Compute-->Electrostatics-->Compute Potential Using APBS

This will open a window with a lot of blue ink. When the scripts finish chugging, click OKAY and your molecule should have hydrogens added to it.



3. Goto Compute-->Electrostatics-->Map Potential to Surface

 

And there you go. Simple, right? You could make it harder if you want.
You could change the colors by double-clicking on the color scale-bar in you viewer. 

And there are plenty of other settings to play with along the way. The best way though, is to just use the standard settings, which will yield similar results as the other programs. That's the beauty of PMV, you can keep it simple, but you can also tweak the model ad nauseam if you wish.