Map Methods

Electron & EM Density Map Methods

Simplified Jmol Density Map Command.

The implementation in FirsGlance (described in sections I and II below) was coded before Bob Hanson implemented a simplified command syntax. Following Hanson's enhancements to Jmol, after selecting the atoms of interest, the simplest command would be:

isosurface within 3 {selected} density

This command automatically determines whether an X-ray or EM map matches the currently loaded PDB identification code, obtains the relevant box of density data, and generates the map isomesh out to the specified "within" distance in Å. The Jmol command manual contains further documentation. Therefore, the more complex commands described below, that were implemented before these enhancements were implemented, could now be simplified.

However, the Ajax calls (see below) used to check availability of a map enable FirstGlance to alert the user when a map is not available, before opening the map display browser tab. So those Ajax calls remain desirable.

I. X-Ray Diffraction Electron Density Maps.

I.A. Checking availability of the X-ray map.

Crystal X-ray diffraction electron density maps are are archived in PDB-Europe (PDBe) in ccp4 format. The presence or absence of a map is determined with an Ajax call (see openEDM() in control2.js) to this API:

https://www.ebi.ac.uk/pdbe/api/pdb/entry/files/6zx4

This returns a block of file URLs. If it includes "ccp4" then the map is available. If not, FirstGlance alerts the user with an explanation. The wwPDB began requiring the deposition of structure factors (from which maps can be generated) in 2008. Before 2008, it was optional whether to include the structure factors in a deposition.

I.B. Displaying the X-ray map.

The all-features map (2Fo-Fc) at 1 sigma is displayed by FirstGlance using a Jmol command of this syntax:

isosurface rmsd 1 within 3 {selected} eds

"isosurface" asks Jmol to generate an isosurface. For density maps, the default is an isomesh, which could also be specified explicitly by adding "nofill mesh" to the end of the command.
"rmsd" specifies the contour level (cutoff) in units of standard deviation (SD, sigma).
"within 3" means show the map up to 3 Å from the selected atoms.
{selected} specifies that only the map within the specified distance of the selected atoms should be displayed. Jmol determines the coordinates of a "box" of density values appropriate for the selected atoms, and requests only those values, which is very fast (in comparison to downloading the entire map).
"eds" means that the 2Fo-Fc ccp4 map should be obtained from PDBe.
For 1ijw, with only residue Phe169:C selected, Jmol automatically fetches a limited "box" of density values from the full map with a URL such as this:
```
https://www.ebi.ac.uk/pdbe/densities/x-ray/1ijw/box/16.5000,-2.7960,-2.062/25.751,9.2800,6.798?space=cartesian&encoding=bcif
```

The difference map (Fo-Fc) at 3 sigma is displayed by FirstGlance using a Jmol command of this syntax:

isosurface rmsd 3 within 5 {selected} edsdiff

"5" means show the map up to 5 Å from the selected atoms. (The default is 3 Å.)
"edsdiff" means that the Fo-Fc ccp4 map should be obtained from PDBe.

For 1ijw, with only residue Phe169:C selected, this command fetches a limited "box" from the full map with a URL such as this:

https://www.ebi.ac.uk/pdbe/densities/x-ray/1ijw/box/14.5000,-4.796,-4.0620/27.751,11.2800,8.798?space=cartesian&encoding=bcif&diff=1

II. Electron Microscopy Density Maps.

II.A. Checking availability of the EM map.

EM maps are archived in the Electron Microscopy Data Bank (EMDB; emdbhelp can be contacted via ebi.ac.uk) in "map" format. The presence or absence of a map is determined with an Ajax call (see openEDM() in control2.js) to this API:

https://www.ebi.ac.uk/emdb/api/search/fitted_pdbs:"6nef"?fl=emdb_id,map_contour_level_value&wt=csv

When the map is present (example: 6nef), this returns

emdb_id
EMD-9357,0.06

When the map is absent (examples: 3izp, 1ucu), only the first line is returned. FirstGlance alerts the user when the map is absent.

II.B. Displaying the EM map.

Bob Hanson has built a lot of convenience into Jmol's command for displaying EM maps. The map is displayed by FirstGlance using a command of this syntax (quotes required):

isosurface cutoff 0.06 within 3 {selected} "*em/"

"cutoff" is the density level for contouring the isomesh. The default cutoff is specified by the authors of the map, and is obtained from the above Ajax call (0.06 in the example given). The cutoff value is density units, not sigma. Typically, the default is roughly 10 times sigma in order for the map to look similar to X-ray maps at 1 sigma.
"*em/" specifies EMDB at ebi.ac.uk.
Jmol first uses the above API to obtain the EMDB map accession number for the currently loaded PDB ID.

Jmol then obtains the appropriate "box" subset of the map densities using a URL of this form:

https://www.ebi.ac.uk/pdbe/densities/emd/emd-9357/box/-9.455,-6.719,-2.0330/7.782,13.695,13.788?detail=6&space=cartesian&encoding=bcif#-cutoff=0.06