Jun 17, 2010

Distinct Molecular Surfaces Per Chain

How you decide to distinguish between chains in a molecule is really up to taste, but I think there is room for improvement in legibility. Most scientists distinguish chains by color. I do too. But we can go farther, and perhaps, do better.

By default, molecular surfaces are calculated with disregard for individual chains:

This is actually more true to 'real life' or 'in situ'. The water molecules defining the surface of a protein have no regard for chains. They simply pass over. But we operate 'in silico', and afforded the opportunity to distinguish with clarity between the molecular surfaces of chains. Perhaps for the better in the end for discovery- or at least another arrow in our quiver.

Here is a side by side comparison:

I think it is clear from the screen shots above that calculating the molecular surface per chain can be a positive augmentation of the representation.

So, without further adieu, I present the simple trick:

1. While in the computeMSMS popup menu, de-select the 'Per Molecule' check box.

2. In that same menu, be sure to rename the 'Surface Name' for each chain.

That's it!

Another quick tip is that you can reach the ComputeMSMS menu by right-clicking the radio buttons in dashboard:



Jun 7, 2010

Aligning Small Molecules

From there:  to here:

Aligning two small molecules is useful and necessary when studying the similarities of form and character of two distinct molecules. Here's one way of doing that in PMV.


2. Select ADD PAIRS.

3. Turn the  BY STRING mode on. You could do this by picking atoms by hand as well. But I find the selecting by string is faster if your molecules have enough similar points (3).

4. The two molecules that I am aligning are methionine and glutamate. I know that they share at least their backbone atoms and the beta carbon "CB". All I need is 3 atoms for an alignment, so I just type "backbone" under the ATOM heading for the REFERENCE and MOBILE nodes. Note that the reference molecule will stay put, while the mobile molecule will be aligned onto the reference molecule, as you might expect.

Also note that by clicking SHOW you will see little blue and red stars over the reference and mobile atoms.

Click OKAY.

5.  Now click CREATE PAIRS  in the superimpose window.

 6. Your molecules should be aligned and you can  DISMISS the "pairwise superimposition" window.

Have fun, 
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