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About the PDBj Electron Density Map Viewer


The Electron Density Map (EDM) viewer allows the display of electron density maps together with molecular models. The viewer is integrated into the Mine PDB Browser. The availability of pre-calculated maps is indicated on the search Result Page by text links, on the Summary Page of a selected structure and on the Experimental Details Page by a text link at the bottom of these pages. At the moment, not all the maps are available, because of lacks of the old structure factors that were not deposited or technical problems at the PDBj procedures, which will soon be solved. Clicking on these links will bring up a page with a jV applet and clicking thecreate mapbutton on this page will display an electron density map. The appearance of the electron density map as well as several associated parameters may be modified to override default values.

Electron densities may be displayed in either one of two different styles: the first (and commonly used) style are electron density contours, the second style are electron density isosurfaces. Electron density contours are spatial lines connecting points with the same density value. Usually these are created by contouring two-dimensional slices through the map oriented with one crystallographic axis normal to the slice. Doing so for each of the three axes in turn and displaying the resulting lines together creates the appearance of a three-dimensional volume outlining the electron density. This presentation style is often colloquially referred to as chicken-wire presentation, for obvious reasons. The second style finds the isosurfaces of constant electron density and displays this surface through a series of triangles which, when shaded, produce the appearance of a solid volume. Graphical manipulations may make this volume appear translucent to reveal the enclosed part of the structural model.

While it is possible to calculate electron densities for any molecular structure, crystallographers usually are interested in maps based on experimental diffraction data. Necessary experimental data are available for roughly half of all deposited structures and for about 95% of these maps can be successfully calculated.

[Electron Density Map Basics]

Electron densities can be probed by the scattering of X-rays. This is usually done by creating crystals, containing many trillions of molecules arranged in a regular three-dimensional pattern. When this pattern is illuminated with X-rays, diffraction of the X-rays occurs. The diffraction pattern encodes the information about the electron density distribution in the crystal. The diffracted rays are themselves, like the incident X-rays, electromagnetic waves with amplitude and phase and form a three-dimensional pattern, known as the reciprocal lattice. They are an indirect image of the electron density and are related to it by a Fourier transform.

To recover the electron density from this diffraction pattern by inverse Fourier transform, both amplitudes and phases are needed. Experimentally usually only the amplitudes can be measured. The phase information remains hidden within these amplitude data and has to be recovered by computational techniques, often requiring additional measurements. This situation is known as thePhase Problem in Crystallography. It is indeed a problem, because the phases influence the electron density to a much larger extent than the amplitudes do.

[Calculating Electron Density Maps from Models]

If experimental amplitudes and a (maybe preliminary) model are available, the experimental amplitudes (often called Fobs) can be combined with the calculated structure factors (either using only the phase phicalc or both the amplitude Fcalc and the phase) to generate electron density maps.

The most common types of maps are Fobs maps (amplitude = Fobs, phase = phicalc), (2Fo-Fc) maps (amplitude = 2*m*Fobs-D*Fcalc, phase = phicalc) or (Fo-Fc) maps (amplitude = m*Fobs-D*Fcalc, phase = phicalc). m and D are weighting factors, varying with reflections and containing information about the accuracy of the model and/or the data.

To obtain the phases phicalc, we use the available model, apply random coordinate shifts of the order of 0.2 Å and random B-factor shifts of 10A^2 to individual atoms to deliberately introduce errors and then refine these models by refmac5, trying to maximize the agreement between Fobs and Fcalc. This process is known as structure refinement and its purpose, together with the randomization, is to reduce the influence of the model on the phases.

We then calculate (2Fo-Fc) maps, using the experimental data Fobs that were deposited and Fcalc, phicalc, m and D obtained from the refined model. The extent of the map is chose to cover the whole molecule plus a border margin of 2.5Å on either side (along the axes) of the model.

[Using the Electron Density Map Viewer]

At the right of the jV picture frame, Parameters for Electron Density Map are input. By default, if nothing else is specified, electron density contours will be calculated for a box of size 10×10×10 Å^3, centered at the center of the calculated map. The contour level is chosen as 1 sigma of the map, which is usually a good value, corresponding to a electron density of about 0.4-0.45 electrons/Å^3. Usually molecular density values are within a range of about one to five sigma, except for heavier atoms, like sulfur or metals, that may go up to ten to fifteen sigma. The default color is cyan and the transparency of isosurfaces is set to 0.5 (only used for isosurfaces). Colors are specified as triples of red(R), green(G) and blue(B), each between zero and one.

After setting all the parameters, pushcreate mapbutton, and the electron density will appear.
When a user wants to undisplay the ED map from the view panel, click the right-button of the mouse on the view panel and select File -Display -(ED map file name, **.xml.gz).
When a user wants to completely delete the ED map, push the button ofDownload/Delete the map, locating on the right side of the view panel. Then, a new pop-up window, Electron Density Map Download/Delete Page, appears showing a file Table, and pushdeletebutton for the corresponding ED map file on the Table.
When a user wants to download files: structure factor, refinement, and edmap file for jV, push the button ofDownload/Delete the map, locating on the right side of the view panel. Then, a new pop-up window, Electron Density Map Download/Delete Page, appears showing a file Table, and push button for the corresponding file on the Table.

[Other Parameters for the Electron Density Map Viewer]

Other box centers can be chosen, based on atom names or cartesian coordinates x,y,z. Atom IDs consist of the chain ID, the residue number and the atom name. They can be found by clicking on an atom in the display. If a chain ID is blank, X should be used instead, as that is the value generated by the refinement program (refmac/CCP4) for such cases. At the moment, when a chain ID box is left blank, X will be automatically sent to the program.If the contour script fails to find the atom specified or if the cartesian coordinates entered are outside of the map limits, it will fall back on the default value.

Box sizes should not be chose too large for two reasons: having a too large box will obscure more than reveal due to overlap along the line of sight. Furthermore, large boxes will take longer to process. While contours are not critical, usually taking fractions of a second to a few seconds even for large boxes, generation of isosurface will take excessive amounts of time if the box size is too large. 10 Å will usually require about three to five seconds, but 20 Å or more might take up to a few minutes. These are value for single users. If multiple users simultaneously request maps, these times will grow as the server is a single-CPU system.

Parameters not variable here may be accessed through the command window of the viewer. Maybe the most valuable commands are:

stereo on/off control side-by-side stereo display
slab on/off control size of slab along line of sight
cpk value set atom radius tovalueÅ
wireframe value set bond radius tovalueÅ

[Available files]

For each entry available within the EDM service, a structure factor file and a refinement file can be downloaded. Also, for a selection of the entries a ccp4 formatted file is available. The entries for which a ccp4 file is available are listed in a file on our ftp.

Finally, given a user's query the EDM service can generate a map for a given area. This file, in PDBj's polygon xml format, can also be downloaded.

[System-specific notes]

The use of the viewer requires that a Java runtime environment be installed.

The viewer has successfully been tested under Windows (XP and 7), MAC OS X and under Linux (RedHat 8.0 and Mandrake 10.0 - Opera and Mozilla).

Contact to PDBj

2012-07-13 (last edited: yesterday)2015-02-26
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