Electron Density Puzzles

[LociOiling]

As also mentioned in chat, I found that electron density info for many proteins is out there on the internet. There's a "PDBe", which is separate from the PDB hosted at rcsb.org.

There's a LiteMol viewer which can display density along with a protein. It's available at http://webchemdev.ncbr.muni.cz/Litemol/Viewer/

The user interface is a little confusing, but there's tree structure on the left. The options for the selected node of the tree are shown on the right.

You start with the "root entity" node, enter the PDB id of the protein you want under "molecule" on the right, and click "add". (PDB 1CBS is there as a suggestion.) That gets you the typical protein viewer display.

To see the density, re-select "root entity", and again enter the PDB id, this time under "density data from PDBe". When you click "add", the density gets downloaded and processed.

By default, density is displayed around a selection, so you have to click on the protein to see anything. When you see density, there are several different types displayed. Some density is represented in a solid view, some is wireframe.

You select the nodes from the tree structure and adjust how different types of density info are displayed. You can also hide density using the "eyeball" on a node.

I haven't deciphered all the density types, but I believe the main idea is comparing the density data to what you'd expect from the protein model. The greek letter σ (sigma) appears in various spots, which I suspect refers to standard deviation units. I'm guessing it's similar to the threshold setting in Foldit, a higher sigma would be like a lower ED threshold.

There's also "Fo-Fc" and "2Fo-Fc" density, again assuming those involve comparison, but I'm not clear on the differences, but "Fo-Fc" gets wireframe by default, and "2Fo-Fc" is solid.

Bottom line, LiteMol is oriented toward assessing how well a protein model and its density match. That's a little different than what we do in Foldit, trying to fit the protein to the density. Still, it seems like the option to display density within a certain distance of a selection would be useful in Foldit. It's a little similar to shift-Q, but the protein and density seem less likely to go out of focus as you rotate.

There are lots of other settings and options in LiteMol, and other viewers may have similar functions. Further investigation pending….

See also:
*Electron density map (EDM) - http://proteopedia.org/wiki/index.php/Electron_density_map
*Interactive EDM demo - http://www.bioinformatics.org/molvis/edm/

[rmoretti]

You're correct about sigma. It does have to do with confidence levels (standard deviation). By varying the sigma threshold, you can look at just the parts of the density we're most sure of versus the bits of the density which are a bit more fuzzy.

The "Fo-Fc" is a "difference map". That is, it looks at the difference between the observed density (represented by "Fo") and the computed density ("Fc"). This shows contours of "positive density" where there's experimental data not represented by the model and "negative density" where the model predicts there should be density, but where no density is observed in the experiment. This can be used to home in on regions of the model which aren't representing the data well. (The method by which one calculates an Fo-Fc map is somewhat complicated and time consuming, which is why Foldit doesn't provide it as an option.)

The "2Fo-Fc" is an attempt to combine the Fo-Fc map with a "standard" electron density cloud. Whereas an Fo-Fc map will show no density where the model matches the experimental data, a 2Fo-Fc map will show a "normal" density cloud. But adding in the Fo-Fc component will help highlight/adjust the portions of the density where the model isn't matching the experimental data.

I've haven't read it in full, but https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5051661/ seems to be an open-access paper which attempts to do an introductory-level description of electron density maps.

And for the really enthusiastic, Gale Rhodes's "Crystallography Made Crystal Clear" is an excellent introductory textbook on X-ray crystallography.

Though I should clarify that many of the electron density clouds we're providing with Foldit are produced via Electron Microscopy instead of X-ray Diffraction. At a superficial level these densities are similar, but details are quite different in how they're produced. (For example, technically there's no such thing as an Fo-Fc or 2Fo-Fc map for EM density. There's similar things you can calculate, but Fo-Fc and 2Fo-Fc are strictly speaking just for diffraction experiments.)

[jeff101]

In Foldit, when you tab on a particular residue and the
"Segment Information" appears, what does a negative Density
subscore mean? I assume a positive Density subscore is
better. Do different amino acids have different maximum
possible Density subscores that would be the same in all
Foldit puzzles? Are these maximum values known? Can you
post a chart of them somewhere?

Also, do you know of any programs that will calculate model
electron densities (Fc above?) for a given pdb file? Should
the model electron density be the same whether one measures
it with Electron Microscopy or X-ray Diffraction?