Opacity

Sometimes you need to see what's below the surface. Here is one way: lower the opacity of the surface... & here is how:

1. Start with a Molecular surface, and a ribbon. Calculate these under Compute--> MSMS, and Compute--> Secondary Structure-->Ribbon. Color the Ribbon by Secondary Structure.

2. The surface is now hiding the ribbon. To see both the ribbon AND the surface, Open the DejVu GUI.

3. Select the MSMS-MOL surface.

4. Under 'Material' deselect the 'inherit' property and then click the 'Front' box.

5. At the bottom of this Material Editor, there is a slider that controls opacity. Lower the opacity to about 50%.

6. Now you can see both your ribbon and your surface.

-Jon Huntoon

Electron Density Map

Here is how you can read and display an electron density map. These are important  to look at if you are to be critical of a particular PDB structure. 

1a Load PDB

1b Download the corresponding CCP4 file from PDB.

 

2a Create a Vision Network. 

 (middle button, boxes & lines, not the sunglasses button)

2b Load the Vis and Vol Libraries from Libraries--> Load Libraries....

 

2c Drag the following 'nodes' on to the blank 'canvas':

- 'Read Any Map' (Load CCP4 here) -from Vol Library (grey)

- 'Sample' (use a level 3 or two) - from Vol Library

- 'UT iso-contour' From Vol Library

- 'Ind Polygons' -from Vis Library (yellow)

- 'PMV Viewer' - from PMV Library (purple-ish/blue?... hmm. Periwinkle!)

(it helps to use the search box  to find these nodes)

Connect these nodes by dragging lines from the output ports (bottom square things) to the input ports(top square things) (colors should correspond [mostly]):

3 Double-click the UT iso-contour 'node' to see the isocontour graphs. Looks like this:

4 Drag the black vertical line to Pick an iso-value that suits your purposes. It will be hairy, so you may want to...

5 Open DejaVu  (it's the left-erly button with a cube, sphere and pyramid) to adjust opacity and or clipping  of the IndPolygons geometry  you just created!

And you can end up with something like this or (probably) better. Explore around. Have fun. Get good.

--

Jon Huntoon

ADT/MGLTools freezes on my Intel Video Graphics Card!

Apparently,

Intel launched those cards prematurely. They weren't ready for Vista's
high-end graphics uses. You should try downloading the latest driver
from Intel.

Also, try downloading MGL 1.5.4. This is the most up-to-date. It's
your best bet even though it's beta.

Unfortunately, this may not work. You may need to buy a better
graphics card. nVidia and ATI are the best.

Another last-ditch attempt is to install linux and use the linux
version of MGL tools.

It's a challenge developing software that is completely free. Free
libraries can be out of date with hard ware, and hardware drivers can
sometimes ignore old(free) libraries. MGLTools will move to python 2.6
that should fix many of these problems, but the implementation will
take a couple months.