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Here is a tour of methods for displaying volume data sets usinginteractive graphics programUCSF Chimera.Data for example images comes from
- EM DatabankandEM Navigator- Electron microscopy density maps
- VIPERdb Cryo-EM Database- Electron microscopy density maps
- Uppsala Electron Density Server- Crystallographic density maps
- Protein Data Bank- Molecular models.
Extracting and Viewing Subregions
| Segment mouse mode (video) | Segment and fit (video) | Box around marker | Plane topography |
| =0?'images/planes.gif':'images/plane0.jpg')' width=229 height=153 /> | |||
| Mask to surface | Rotated subregion | Plane display | Split map by color |
| Erase outside sphere | Zone display | Slicing and capping | Slab clipping |
| Icosahedral slice | Erase octant | Hand erasing | Subregions |
Fitting and Modeling
| Place spherical markers(video) | Find symmetry axis | IMOD surfaces | Symmetric fitting |
| Fit map in map | Fit model in map | Place markers | Icosahedral cage |
Filtering
| Smooth mask (video) | Binning |
| Hide dust | Median filter | Fourier transform | Gaussian smoothing |
Measurement
| Local correlation(video) |
| Degree of symmetry | Measure volume | Path length | Shell radius |
Coloring
| Color connected surface | Color zone | Radial coloring | Electrostatic potential |
| Color by density value |
Appearance
| =0?'images/emd_1283_1284.gif':'images/emd_1283_1284.jpg')' width=160 height=200 /> | |||
| Morph map | Ambient occlusion lighting | Box face capping | Square mesh |
| Close boundary holes | Surface smoothing | Multiple contour levels | Display styles |
Work in Progress
This web page is being developed. Some topics not yet covered are:
Segment mouse mode | (June 16, 2010, version 1.5 daily build, details, video) |
Density maps can be segmented by clicking on regions with the mouse anddragging to control the extent of the region. The dragging sets a densitylevel and connected density above that threshold forms a region. Regionsobtained by watershed segmentation are shown and joined using these mouseactions.To turn on the mouse mode first display the Segment Map dialog,
Tools / Volume Data / Segment Map
press the Options button, and enable
Group with mouse [button 3]
Button 3 means the right mouse button of a 3-button mouse. Select themap to segment in the Segment map menu at the top of the dialogand click on density map (using button 3). The first click calculatesand displays the watershed regions and can take some time. Then click anddrag on specific regions to group them into segmented objects. Groupswill be indicated by color, and new regions will not extend into alreadygrouped regions. Releasing the mouse button shows the objects touchingthe last segmented object. Clicking on the background will show theremaining ungrouped regions. A second click on the background will showall regions, grouped and ungrouped.
This method was developed for rather well separated objects touching insmall places (bacteria in termite gut). It will be very slow for more than100,000 watershed regions (local maxima) so smoothing the volume data beforehandmay be necessary to reduce the number of regions. On Mac OS 10.6 poor systemgraphics driver memory management makes the region display unusably slow formore than 5000 displayed regions.
Segment and fit | (June 16, 2010, version 1.5 daily build, details, video) |
Density maps can be segmented by computing watershed regions of and groupingthem using according to overlap with watershed regions of smoothed copiesof the map. This method works well on single-particle EM reconstructionsof molecular assemblies.
Open the map and set a desired contour level. Only parts of the map abovethe displayed contour level will be segmented. Press the Segmentbutton on the Segment Map dialog.
Tools / Volume Data / Segment Map
Colored regions will be shown. If the aim is to make the regions correspondto individual molecules and the computed regions are too small, pressing theGroup button will perform another round of smoothing and grouping toproduce fewer regions. The Ungroup button will make smaller regionsundoing the previous smoothing round. If regions are selected with the mouse(ctrl-click and shift-ctrl-click) then the Group and Ungroup buttons insteadjust join or split apart the selected regions.
The default settings in the options panel (Options button) dothree rounds of Gaussian smoothing with standard deviations 1, 2, and 3grid spacings to group the watershed regions of the unsmoothed map. Awatershed regions is the set of points that reach the same local maximumof the density map following a steepest ascent walk.
This method will be very slow for more than100,000 watershed regions (local maxima). For very high resolution mapssmoothing the volume data beforehand may be necessary to reduce the numberof regions. On Mac OS 10.6 poor systemgraphics driver memory management makes the region display unusably slow formore than 5000 displayed regions.
To fit a molecular model into a segmented region,show the Fit to Segments dialog
Tools / Volume Data / Fit to Segments
Select the molecule file from the Structure to fit menu if it is inthe same directory as the density map. Or you can open the structure usingthe normal Chimera File / Open... dialog and then select it in themenu. Then select the region to fit to (ctrl-click on the region), andpress the Fit button. This aligns the principle axes of the moleculewith those of the region density and then does a local rigid optimization.
Box around marker | (2001, version 1.0, details) |
To limit map display to a box around a selected marker use the volumedialog Atom Box panel, shown using volume dialog menu entry
Features / Atom box
Enter a padding value which is the distance from the center of theselected marker to the edge of the desired box and press the Boxbutton. This restricts the map display to that box. The subvolume canbe saved to a new map file with volume dialog menu entryFile / Save Map As....
See the marker placementdescription for how to create markers. If more than one marker isselected when the Box button is pressed then a single subregionis shown enclosing all the markers with minimum distance from theboundary to any marker equal to the padding value.
Plane topography | (November 2007, version 1.2475, details) |
The topography command creates a surface from a volume plane where theheight of the surface above the volume plane is proportional to thedata values. After displaying asingle plane of volume data, the following Chimeracommand
topography #0 height 10
will create the surface. To enter the command show the Chimeracommand line with menu entry Favorites / Command line. The #0parameter is the volume model number. The model numbers are listed inthe Model Panel dialog, shown with menu entryFavorites / Model Panel. The height value specifies the heightof the surface from minimum data value to maximum volume data value.It is specified in the length units associated with the map, such asAngstroms.
By default the surface is colored red to blue from lowest to highestpoints. This and several smoothing / interpolation capabilities arecontrolled by additional command options that are described in theUser's Guide.Different color schemes can be applied using the color by heightcapabiliy of the Surface Color tool(menu entry Tools / Volume Data / Surface Color).
Mask to surface | (October 2007, version 1.2467, details) |
You can extract part of a map bounded by a surface using the maskcommand. The surfaces can be drawn in another software packageIMOD and imported into Chimera. Or surfaces createdwithin Chimera such as the contour surface of a Gaussian filtered map canbe used.
Display the command line with menu entry
Favorites / Command line
then type a command such as
mask #0 #1
to copy part of volume #0 bounded by surface model #1. Model numbers startat zero and new models are assigned the next available number. The model numbersare listed in the Model Panel dialog, shown with menu entryFavorites / Model Panel. To mask to just a single surface object inand IMOD segmentation use a command such as
mask #0 sel axis 1,0,0
This command copies part of volume #0 within the selected surfaceprojecting along the x axis. The surface object is selectedusing the left mouse button with the ctrl key held down.The projection axis (default z) effects how holes in the surface arehandled. Points within the surface when viewed along the projection axisare taken.
The new volume with zeros outside the surface can be saved to afile using volume dialog menu entry File / Save map as....The map will usually be smaller than the original map unless thefullmap option is used with the mask command. The origin willbe specified in the new volume file so that it will align with theoriginal map.
Rotated Subregion | (September 2007, version 1.2443, details) |
You can extract part of a map that is not aligned with the axes of theoriginal map. This is useful for chopping out objects in tomograms thatare not aligned with the map axes. Open the map, then use theSubregion Selection panel of the volume dialog (in the Featuresmenu). Turn onSelect subregions using button 2 and drag a green selection boxaround the part of the map of interest with mouse button 2. Then click the
Rotate selection box
checkbutton. This freezes the map (and any other models) so that you canrotate only the green outline. To move the green outline box side to sideclick and drag outside the bounds of the box with mouse button 2. Hold downthe shift key at the same time to move the box in the z direction.Press the
Resample
button to create a new volume data set with those bounds. The data canbe saved to a separate file using volume dialog menu entryFile / Save map as.... The rotation is saved in MRC and Chimeraformat map files and will align with the original data when opened insubsequent sessions. Uncheck the Rotate selection boxbutton to allow normal rotation of all models.
This procedure interpolates (resamples) the original map on a new gridwith voxel spacing given by the Resampling voxel size listed in thesubregion panel of the volume dialog. You may wish to change that to a valuesmaller than the original map voxel size to avoid reducing resolution.
Plane display | (July 2007, version 1.2430, details) |
Single planes can be displayed with gray scale rendering, frequentlyuseful for tomography data. Use the Planes panel of the volumedialog shown with volume dialog menu entry
Features / Planes
Turn on the plane checkbutton next to the plane number and slider.Planes perpendicular to the z, y, or x axes can be displayed using theaxis menu and a slab containing more than one plane can be shown usinga depth entry greater than 1. The Play button cycles throughthe planes, reversing direction when the end planes are reached.
Plane display uses solid rendering and sets the displayed subregion toshow just the desired plane. The yellow line on the histogram controlsthe brightness of different data values.
Split Map by Color | (October 2007, version 1.2458, details) |
A map colored with the color zone tool can besplit into separate maps, one for each color. The splitting is doneusing the
Split Map
button on the color zone dialog.The splitting creates a separate map for each color zone color of themap currently displayed in the volume viewer dialog. If the displayedmap is a subregion then the newly created mapsinclude just that subregion. The new maps always includes all datafrom the subregion even if the original map was displayed withsubsampling. The new maps are given names with 0,1,2,... appended tothe original map name. The original map is undisplayed although itremains open. The map with 0 appended is the uncolored part of theoriginal map (i.e. outside of the color zone) and the other colors areordered randomly. The new maps can be saved (one at a time) to filesusing volume dialog menu entry File / Save Map As....
Erase Outside Sphere | (November 2005, version 1.2186, details) |
A map can be set to zero outside a sphere to extract a spherical piece.This is useful for virus particles. This uses theVolume Erasertool, menu entry
Tools / Volume Data / Volume Eraser
Adjust the sphere position with the mouse, and sphere radius with the sliderin the Volume Eraser dialog. To set the data values outside the sphere tozero use keyboard accelerator eo ('erase outside'). Use of keyboardaccelerators is turned off by default. Turn them on with menu entry
Tools / General Controls / Accelerators On
Then type eo in the main graphics window. You do not press the Enter key.This keyboard accelerator is currently the only way to erase outside a sphere.There is no equivalent dialog button or Chimera command.
The image shows the dodecahedral penton particle from human adenovirus type 3,EM Database entry1178
Zone display | (August 2005, version 1.2154, details) |
Pixel Pop Defense Zone Mac Os 7
Volume data can be displayed just within a specified distance of selectedatoms or markers. Check the Region switch at the top of thevolume viewer dialog (menu entry Tools / Volume Data / Volume Viewer).This expands the dialog to contain extra buttons. Select atoms froman already opened PDB molecule with the mouse by holding down thectrl key and dragging a box or clicking individual atoms. Thenpress Zone. This restricts display of the volume surface toonly show parts within 2 angstroms. The range can be changed usingthe slider below the Zone button.
Atoms can be selected in many different ways. Menu Select / Chain/ A can be used to select chain A. To select a single residuectrl-click on an atom of the residue then press the up arrowkey to extend the selection to the containing residue. TheSequence dialog (menu Tools / Structure Analysis / Sequence)shows the amino acid sequence using one letter codes that can beselected to select ranges of residues.
The image shows an RNA / DNA hybrid, the base pairs at both ends beingRNA and the 8 base pairs in the middle being DNA. Thecrystallographic density map used to solve this structure is shownaround just one strand of the double helix. (PDB 100d and denisty map from theUppsala Electron Density Server).
Slicing and capping | (August 2005, version 1.2154, clipandcapdetails) |
A map can be sliced in half with a plane at an arbitrary angle using
Tools / Depiction / Per-Model Clipping
Turn on the Enable clipping switch in the dialog that appears.The cut plane can be moved by turning on the Adjust clipping with mouseswitch near the bottom of the Per-Model Clipping dialog. The hole left byslicing a surface can be covered with a cap using
Tools / Depiction / Surface Capping
Turn on the Cap surfaces at clip planes switch in the surfacecapping dialog. The cap can be displayed as mesh and with a differentcolor using dialog settings.Shown is a ribosome bound to tmRNA (a combined tRNA / mRNA sequence)(EM database entry 1122). This sequence unclogs ribosomes blocked by defectivemRNA.
Slab clipping | (August 2005, version 1.2154, clipandside viewdetails) |
A slab of a volume data set can be displayed using
Tools / Depiction / Per-Model Clipping
Turn on the Enable clipping switch and the Use slab modeswitch. The location of the slab in the data set can be changed byturning on the Adjust clipping with mouse switch and dragging withthe mouse. Slabs parallel to the screen can be obtained with
Favorites / Side View
This shows a view of the data from the side. The small yellow squareat the left represents your eye. The two vertical yellow lines arethe near and far clip positions. These can be dragged with the leftmouse button so they are close to one another. Drag the left (nearplane) line with the middle button to move both lines together. Dragthe right (far plane) line with the middle button to change the separationbetween the planes (thickness of slab).
A 5 angstrom thick slab of Phage T4 is shown colored by density values(EM database entry 1075).Yellow is low density and blue is high density using theSurface Color tool. Concentric layers of thevirus DNA are visible.
Icosahedron slice | (November 2005, version 1.2186, icosahedronandsurface colorandorigindetails) |
| Movie |
Icosahedral and spherical slices of a density map can be shown using theIcosahedron Surface tool and the Surface Color tool, menuentries
Tools / Higher-Order Structure / Icosahedron Surface
Tools / Volume Data / Surface Color
This is intended for looking at sections of icosahedral virus particles.The icosahedron surface tool displays a surface linearly interpolated betweenan icosahedron and a sphere, and the surface color tool colors that surfaceaccording to density map values. Use the Show button on theicosahedron surface tool to create the surface. Set the subdivision factorto 64 to produce a fine mesh. Colors are assigned to individualsurface vertices so fine mesh is needed to see short-range densityvariations. Use the Open map data... button on the Surface Colortool to select the density map, press the Set full range colormap valuesbutton, and then the Color button.
If the density map is not centered at the origin (where the icosahedron iscentered) then you can recenter it. Show the Volume Viewer dialog.
Tools / Volume Data / Volume Viewer
Select the density map from the Data menu at the top of the volume dialog.Then use volume dialog menu entry
Features / Origin and Scale
and change the origin values. The origin specifies the location of thecorner of the map in xyz coordinates. To place the center of the map at(0,0,0) position the corner at -(voxel size)*(map size - 1)/2. Press theEnter key in one of the Origin entry fields or press the Show button atthe bottom of the dialog to use the new origin.
Rice dwarf virus(EM database entry 1060). Movie shows density at varying radii.
Erase Octant | (November 2005, version 1.2186, details) |
To erase a box subregion of a volume data set, first draw the boxusing the volume viewersubregion selection capabilityand then erase the data in the box using keyboard shortcut eb.Here are details. First open the data. Next use volumedialog menu entry Features / Subregion selection which addssome buttons to the volume dialog. Click on the Select subregionsusing button 2 checkbutton, and then drag a box in the graphicswindow. The 3-dimensional green outline box can be adjusted bydragging faces of the box (not edges and not vertices) with mousebutton 2. Now activate use of keyboard shortcuts with menu entry:
Tools / General Controls / Accelerators On
Now type 'eb' to erase the volume data in the green subregion box.Erasing causes a writable copy of the data set to be created. Seethe Volume Eraserdocumentation in the User's guide for more details.
The data shown is kelp fly virus(EM database entry1154) and it has beenradially colored.
Hand Erasing | (November 2005, version 1.2186, details) |
The volume eraser tool lets you erase data within a sphere. The spherecan be moved and resized, data values inside the sphere can be set to zero.Start this tool with menu entry
Tools / Volume Data / Volume Eraser
The sphere can be dragged using the mouse ctrl button 3.Pressing the Erase button sets the data values inside the sphereto zero. The first erasure causes a writable copy of the data set tobe created. The modified data can be saved using the volume dialogmenu entry File / Save Map As.... There is no undo capability.
The data shown is part of rice dwarf virus(EM database entry1060)and it has been colored with thecolor zonetool.
Subregions | (August 2005, version 1.2154, details) |
| Before cropping | After cropping |
Display can be restricted to a subregion of a data set using the volume viewerdialog. The dialog is shown whenever you open a volume data set or you canuse menu entry
Tools / Volume Data / Volume Viewer.
The checkbuttons at the top of the volume dialog expand the dialog toshow more features. Click the Region checkbutton at the top.Then turn on Select subregions using button 2. Now drag a boxover the desired subregion of the data set in the graphics window andpress the Crop button. Subregions are constrained to be boxesaligned with the volume data axes. You can adjust the green outlinebox by dragging any of the 6 faces with mouse button 2.
The image shows a bacterial toxin pneumolysin that forms pores as largeas 26 nm in cholesterol containing membranes to kill cells.(EM database entry 1107). The colored image usedtwo copiesof the data set, one colored transparently, with coloring by height using theSurface Colortool.
Smooth mask | (October 2012, version 1.7, details, video) |
The vop falloff command smooths the boundaries of masked maps by replacingeach value outside the mask by the average of its 6 nearest neighbor values.The averaging is repeated for 10 iterations although a higher number canbe chosen for smoother appearance or lower number for quicker falloff outsidethe mask. For a map with id number 2 the command would be
vop falloff #2 iterations 10
To show the Chimera command line use menu entry
Favorites / Command-line
The command will create a copy of the map with smoothing applied.Detailsof how the appearance and falloff boundary thickness vary withthe number of iterations have been illustrated with a simple case ofmasking a uniform density to a sphere. For the default 10 iterationsthe drop off to half density occurs over a distance of about 0.7 grid points.
Binning | (June 2009, version 1.4, details) |
The binning filter averages volume data values in 2 by 2 by 2 boxes reducingthe size of the map by 2 in each dimension. This increases the signal tonoise ratio, especially useful for noisy tomography data. Larger bin sizescan be used. Show the volume filter dialog with
Tools / Volume Data / Volume Filter
select Filter Type 'Bin' and press the Filter button. The filter is appliedon the currently highlighted map in the volume dialog and creates a new map.
The new map only contains the displayed subregion of the original map.To make the new map cover the entire original map press the Options buttonand turn off 'Displayed subregion only'. For large maps that do not fitin memory, the new map may not display with a warning about memoryallocation failing. The new map is still valid but only a smaller region canbe shown. The full binned map can be saved with the volume save command(e.g. 'volume #0 save ~/Desktop/binned.mrc') or Volume dialogFile / Save Map As menu entry. This does not require thefull original map to fit in memory since only a single data plane is readand written at a time.
The binning can be done with thevopcommand (e.g. 'vop #0 bin binsize 3') instead of the volume filter dialog.
Hide Dust | (January 2009, version 1.4, details) |
The hide dust tool hides small surface blobs. It does not create a newvolume data set. It provides a clearer view of large connected structures.Use menu entry
Tools / Volume Data / Hide Dust
choose the desired surface and press the Hide button. Disjoint surfaceblobs smaller than the size limit are hidden. The size is the maximumsize along the x, y and z axes in the surface coordinate system. Adjustingthe slider automatically updates the surface display for the new size limit.The Options button shows a panel allowing other size measures: hiding thesmallest N percent of blobs, or hiding blobs enclosing less than a specifiedvolume. Hide dust works on any surface including ones not derived fromvolume data.
Median Filter | (January 2009, version 1.4, details) |
Median filtering reduces noise while maintaining edges. Use menu entry
Tools / Volume Data / Volume Filter
choose filter type Median 3x3x3, press the Filter button. If morethan one volume data set is open then the highlighted one in the volumeviewer dialog will be filtered. A new volume data set is created andthe original volume is hidden. Each data value is replaced by themedian of the 27 nearest values (3 by 3 by 3 box). The iterationsparameter allows applying the median filtering operation more than onetime in succession. Three iterations is frequently useful. The gridpoints on the boundary of the new volume have value 0.The new map can be saved with volumedialog menu entry File / Save Map As....
Fourier Transform | (October 2007, version 1.2458, details) |
To display the Fourier transform of a map use menu entry
Tools / Volume Data / Fourier Transform
This creates a new map that is the Fourier transform (FT) of thevolume dialog active map. The original map remains open inChimera but is undisplayed. The new map contains only the magnitudesof the Fourier coefficients because Chimera does not work with complexvalue maps. The outline box for the FT map is displayed. Values nearthe edge represent high frequency components while those near thecenter represent low frequency components. The FT map is centered atthe center of the original map and its size is scaled to match theenclosed volume of the original map. The physical units along theaxes are reciprocal length so their scaling relative to Chimera lengthcoordinates is not meaningful. If the original map grid plane spacingis not the same for x, y, and z axes then the FT map box will not be acube. The longest dimension of the FT box will correspond to thesmallest grid plane spacing.
The FT map can be used to assess the amount of oversampling in the originalmap (non-zero Fourier coefficients fill only a small sphere). The imageshows the Fourier transform of tomography data(EMDB1155)with the missing wedge caused by limited tilt angles in data acquisition.
Because the FT map does not include phases, applying a second FT willnot reproduce the original map. Therefore erasing frequencycomponents (with volume eraser) cannot be used as a selectivefiltering technique.
The FT map zero wavelength coefficient is set to zero. That is donebecause its value is usually so large that it makes the histogram displayin the volume dialog uninformative because of the empty range ofvalues between the zero term and all other terms covers almost the entirehistogram.
Gaussian Smoothing | (October 2007, version 1.2454, details) |
A map can be smoothed by convolution with a Gaussian of specified width.Use menu entry
Tools / Volume Data / Volume Filter
or in Chimera 1.3 or older versions
Tools / Volume Data / Gaussian Filter
Enter the width of the Gaussian and press the Filter button tocreate a new map. The width is specified in the same units as the map(typically Angstroms or nanometers or grid planes). Chimera only keepstrack of the spacing between grid planes for the map, not the name ofthe physical units. To see grid plane spacing used for the map use volumedialog menu entry Features / Origin and Scaleand look at the voxel size. The Gaussian width specified in the filteringdialog is one standard deviations. The filtering is applied tothe map that is shown in the volume dialog at the time the Filter buttonis pressed.
The original map remains open in Chimera but is undisplayed.Typically the contouring level will need to be adjusted on thesmoothed map to see features of interest even though the Gaussiankernel is normalized to 1. The new map can be saved with volumedialog menu entry File / Save Map As....
Place spherical markers | (June 18, 2010, version 1.4, details, video) |
Spherical markers can be hand placed in a density map, for example, toshow the position and size of vesicles in electron microscopy. Themarkers are place using the mouse and settings in the Volume Tracer dialog.
Tools / Volume Data / Volume Tracer
Markers can be hand-placed on data with low signal-to-noise by viewing asingle data planeand clicking to create a spherical marker and dragging to move or resizethe marker. The useful settings in for this in the Mouse menu ofthe Volume Tracer dialog are
Place markers on surfaces [on]
Move and resize markers [on]
Place markers on high density [off]
Link new marker to selected marker [off]
Also it is convenient to use button 3 (the right mouse button) if youhave a 3-button mouse with a scroll-wheel since the normal button 3 zoomingaction can be done with the scroll wheel.
Clicking on the displayed density will place a marker. Its color and radiuscan be set with fields in the Volume Tracer dialog. It can be moved by clickingon it and dragging. Holding the shift key will allow moving it in the directionperpendicular to the screen. Engaging the caps-lock key allows adjustingthe marker radius by clicking on it and dragging up or down.
The default volume tracer mouse mode settings are more suitable forplacing markers on data with better signal-to-noise such as single-particleEM reconstructions. This use is described here.
Find symmetry axis | (January 2009, version 1.4, details) |
A symmetry axis of a map can be located using themeasure rotationcommand. The basic procedure is to make a copy of the map, rotate it by handto a symmetrical position, optimize that alignment, then measure the axis ofrotation between the original map and the copy. To make the map copyuse volume dialog menu entry
File / Duplicate
Then rotate the map copy by hand about the observed symmetry and optimizeits fit in the original map using theFit in Mapdialog. To determine the symmetry axis accurately it helps to rotateby an angle near 180 degrees, for example, for 7-fold symmetry rotate 3/7or 4/7 of a full turn. To calculate the axis use a command like
measure rotation #0 #1 color orange
where the two maps have id numbers 0 and 1. The axis will be displayed asa rod that is defined as two spherical markersjoined by a cylinder (equivalent to two atoms and a bond). The axis isa new model with its own id number shown in the Model Panel dialog(menu Favorites / Model Panel).The map copy can be deleted. To rotate a map or any Chimera modelabout this axis use a command like
turn #2 45 models #1
where the model id of the axis is 2, the rotated model has id 1, and therotation is by 45 degrees. You can quantify approximate symmetries byplotting the correlation of a map with a rotated copy of itself usingcommand measure correlation.
IMOD surfaces | (October 2007, version 1.2454, details) |
Surfaces enclosing structures in tomography data created in theIMODsoftware package can be displayed in Chimera. Simply open the IMOD binaryfiles with file suffix .imod or .mod using Chimera menu entry
File / Open....
The surfaces are created in IMOD by drawing contours, loops or curves,plane by plane within the map data which are then connected intosurfaces. The file must contain mesh data which can be createdfrom the contour data with theimodmeshprogram.
Individual imod objects can be selected with the mouse. Some Chimerakeyboard shortcuts(enabled with menu entry Tools / GeneralControls / Accelerators On) are helpful for manipulating theseselected objects:
- hs - hide surfaces.
- sf - show surfaces.
- Ds - delete surfaces.
- co - color surfaces.
- ms - show surfaces as mesh.
- fs - show filled surfaces (not mesh).
- Sc - split surfaces into connected components.
- is - invert selection.
- mv - measure volume enclosed in surfaces.
- ma - measure area enclosed in surfaces.
- sd - measure distance from markers to surface.
Placing the mouse over a surface will show the IMOD name for that objectin a pop-up balloon.A map can be masked to within the selected surfaces usingthe mask command. The surfaces canbe colored according to map density using theSurface Color tool.
Symmetric fitting | (October 2007, version 1.2456, details) |
When fitting an atomic model into a map with symmetry, copies of the atomicmodel can be automatically placed to preserve symmetry as the original copyis fit. This helps see steric clashes between neighboring copies of theatomic model as the fitting is performed. Use the command 'sym' tocreate the multiple symmetry-tracking copies of an atomic model. Thiscommand is typed to the Chimera command line at the bottom of the mainChimera window. To display the Chimera command line use menu entry
Favorites / Command Line
The command uses matrices specified in the PDB file header to positionthe symmetric copies. These usually have to be added in a text editor.Each 3 row and 4 column matrix gives a 3 by 3 rotation matrix in the first3 columns and a following translation in the last column. These transformsare applied relative to the map coordinate system.Here is an example for the helical symmetry shown in the above myosin image:
If you have multiple PDB models or multiple maps open you can specify theid numbers of the desired PDB model and map in the sym command. For example,
sym #1 #0
would use PDB model with id number 1 and map with id number 0. Use menuentry Favorites / Model Panel to see the id numbers of the open datasets. The ~sym command removes the symmetric copies.
Fit map in map | (November 2006, version 1.2315, details) |
One density map can be fit within another. The first map ishand-placed using the mouse into the second map, and then a localoptimization of the overlap between maps can be performed. To moveone map with the other held fixed use menu entry
Favorites / Model Panel
Switch off the checkbutton in the first column (heading Active)of the Model Panel dialog next to the map that will be frozen.Now move the other map with the mouse(buttons 1 and 2) to an approximately correct position in the frozen map.
To locally optimize the position of the map use menu entry
Tools / Volume Data / Fit Map in Map
This tool moves and orients the map to maximize the overlap (sum ofpointwise products of map values). It uses a steepest ascentalgorithm and only finds the locally optimal position. Select the twomaps and press the Fit button. The map is moved to the locallyoptimal position after up to 100 steps. The correlation between thetwo maps is reported.
Note that the overlap is optimized, not the correlation. The correlationis just the overlap normalized by the sum of squares of the map values.Because the correlation is calculated only using points within the displayedcontour level of the map being placed, the normalization factor for thesecond map varies according to fit position. So optimizing overlap is notequivalent to optimizing correlation. A noticable consequence is thatthe fit map will be pushed towards higher density regions even if thepattern of density variation does not match.
Fit model in map | (November 2005, version 1.2186, details) |
Atomic models can be fit into a density map by hand with the mouseand a local optimization of the fit position can be performed. To move anatomic model while keeping a density map fixed use
Favorites / Model Panel
Switch off the checkbutton in the first column (heading Active)of the Model Panel dialog next to the name of the density map. Thislocks the map position. Now move the atomic model with the mouse(buttons 1 and 2) to an approximately correct position in the map.
To locally optimize the position of the model in the map use menu entry
Tools / Volume Data / Fit Model in Map
This tool moves and orients the model to maximize the sum of density valuesat selected atom positions. It uses a steepest ascent algorithmand only finds locallyoptimal positions. Select atoms of the model to use in the fit (for example,menu entry Select / All) and press the Fit button. The modelis moved and the average density value and the size of the motion (translationand rotation) are reported in the reply log (menu entryFavorites / Reply log).
The map shown is of E. coli chaperonin(EM database entry1046)and the fit model is PDB1grl.
Place markers | (August 2005, version 1.2154, details) |
| Zone near markers | Color near markers |
Markers can be placed on volume data with the mouse. Use menu entry
Tools / Volume Data / Volume Tracer.
Then hold the ctrl key and click with the third mouse button (rightmost)on the volume surface to drop a marker. A marker will be placed on the firstmaximum of the volume data along the line of sight under the mouse position.The marker appears as a sphere. Links are drawn between consecutivelyplaced markers. Markers and links can be given different colors and radiior can be deleted. Click the Markers button at the top of thevolume tracer dialog to expand the dialog to show these additional controls.
Markers can be used for restricting volume data display to a regionnear the markers (see zone display), or to colorthe volume surface near the markers (see zonecoloring), or their positions can be written to a file (click thevolume tracer dialog Sets button and use Export XML).
The image shows a segment of a two layer tubulin fiber. Alpha and betatubulin proteins have different colored markers.(EM database entries:inner layer 1129,outer layer 1130). The maps have opposite handedness as those shown in thepublicationNature. 2005 Jun 16;435(7044):911-5.This is most likely an error in the deposited data files.
Icosahedral cage | (October 2007, version 1.2466, details hkcage and meshmol) |
An icosahedral reference lattice can be shown for comparison to virus capsids,clathrin cages, carboxysomes and other icosahedral structures. This uses thehkcage command:
hkcage 2 1 linewidth 3 color blue sphere 0.8
The integer parameters h=2 and k=1 describing the arrangement of hexagons andpentagons are described in thehkcage documentation.The cage can have flat triangular facets (sphere 0.0) or be spherical(sphere 1.0) or any radially interpolated intermediate.
The cage is a surface model shown as a mesh. The mesh lines are twodimensional. To make the cage lines cylinders you can make convert thesurface model into a molecular model with the meshmol command whichtakes the model number and the cylinder radius as parameters.
meshmol #0 2.5
The resulting model can be saved as a PDB file with File / Save PDB....
Local correlation | (October 2012, version 1.7,details,video) |
Thevop localcorrmeasures the local correlation between two maps using a moving window ofsize N by N by N grid points (default N = 5). It can be used to see wheretwo aligned maps are similar and where they differ. To compare two mapsuse
vop localCorrelation #0 #1
which will produce a new map containing correlation values (-1 to 1)where the correlation at each grid point is computed over a box centeredat that grid point of N by N by N grid points. This new map can be usedto color one of the original maps using theSurface Colordialog or with the equivalent command
scolor #0 volume #2 cmap 0.8,red:0.9,white:1,blue
To find the local correlation of a molecular model with a map the molmapcommand can be used to make a simulated map for a molecular model. Then the Values at Atom Postionsdialog combined with theRender by Attributedialog can be used to color atomsaccording to the local correlation at the atom positions.
Degree of symmetry | (January 2009, version 1.4, details) |
The measure correlation command can be used to assessapproximate symmetry of a map by plotting correlation of the map witha copy of itself rotated about the symmetry axis as a function ofrotation angle. The command looks like:
measure corr #1 #0 rot #2
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where the map, its copy, and the rotation axis have model id numbers 0, 1 and 2.To create the symmetry axis and a copy of the map refer to thefind symmetry axis description. The command createsa plot in a separate window showing correlation coefficient versus rotationangle. Clicking and dragging in the plot window will rotate the map copyto the corresponding angle and show an vertical line at that position inthe plot window. The plot image can be saved.
Measure volume | (November 2005, version 1.2186, details) |
The volume enclosed by a surface can be measured. This can be usedfor estimating the size of proteins that would occupy that volume.Use menu entry
Tools / Volume Data / Measure Volume.
Select a surface using the menu in the measure volume dialog and pressthe Compute Volume button. If the surface has several disconnectedcomponents, the computed volume is the sum of the volumes of all components.To measure the volume of just one component you can use volumesubregion selectionorvolume erasingto get a surface of just the desired part.If the surface has any holes then no volume will be computed. For a contoursurface, holes will only be present if the high density region hits the edgeof the data set box. In this casezeroing the boundaryof the data set will close the holes.
The image shows the phage p22 tail, EM database entry1119.Subregion selection was used to cut out one of the 6 pods (purple).The boundary of that subregion was zeroed to close a hole where it connectsto the tail body. The volume was displayed in the image using theChimera 2D Label utility (menu entry Tools / Utilities / 2D Labels).
Path length | (November 2005, version 1.2186, details) |
The length of a path created with thevolume tracercan be measured. This is done with keyboard accelerator pl.Keyboard accelerators are turned off by default. To activate them use menuentry
Tools / General Controls / Accelerators On
Then select the path (for example, by dragging a box around it with ctrlbutton 1) and type pl in the graphics window. The path length is reportedat the bottom of the main window status line and also is reported in theReply Log (shown with menu entry Favorites / Reply Log). The pathlength accelerator works on any set of selected bonds. They need not forma single chain.
The image shows a model of the 1056 nucleotide single stranded RNAgenome of satellite tobacco mosaic virus. The path length wasdisplayed in the image using the Chimera 2D Label utility (menu entryTools / Utilities / 2D Labels).
Shell radius | (November 2005, version 1.2186, details) |
The radius of a spherical or icosahedral shell can be measured. Thiscan be used for measuring layers of virus particles. Display theIcosahedron Surface tool with menu entry
Tools / Higher-Order Structure / Icosahedron Surface
The dialog can display a surface linearly interpolated betweenan icosahedron and a sphere. Use the Show button on theicosahedron surface tool to create the surface. The radius of thesurface can be adjusted with the radius slider. With solid displaystyle make the surface transparent by pressing the color button.On the color dialog press the Opacity button, and then adjustthe slider labelled A, 0 = completely transparent, 1 = completelyopaque.
To get a spherical shape or when interpolating between a sphere and anicosahedron, set the subdivision factor to a larger value, forexample, 64. This is needed to produce the rounded shape. Thesphere factor controls linear interpolation between icosahedronand sphere shapes, 0 = icosahedron, 1 = sphere.
If the density map is not centered at the origin (where the icosahedron iscentered) then you can recenter it as described in theicosahedral sliceexample.
The image shows Paramecium Bursaria Chlorella Virus(PDB 1m4x)displayed using the Multiscale tool and a shell of radius 910 angstroms,with sphere factor = 0.42.The radius text on the image was added using the Chimera 2D Labelutility (menu entry Tools / Utilities / 2D Labels).
Color connected surface | (October 2007, version 1.2456, details) |
Connected surface components can be colored and there volume and areameasured using menu entry
Tools / Volume Data / Pick Surface Pieces
The pick surface pieces dialog allows you to choose a mouse button(default ctrl-button-3) and color. Clicking on a surface colors theentire connected surface component under the mouse and reports its volumeand area in the status line and reply log (Favorites / Reply Log).If the level of a volume contour surface is changed, all coloring done withthis tool is lost. There is currently no way to save the coloring.
The example shows a unit cell of x-ray density for PDB model1a0m. Twomonomers have density not connected to any surrounding density at a contourlevel of one standard deviation and have been colored yellow and blue withvolumes reported as 238 and 240 ų.
Color zone | (August 2005, version 1.2154, details) |
| Side view | Oblique view |
Patches of a surface near selected atoms or markers can be colored to matchthe atom or marker colors. Use menu entry
Tools / Volume Data / Color Zone
to show the color zone dialog. Select the atoms from a molecular structureor markers placed with thevolume tracer tool by holding the ctrlkey and clicking on them with the left mouse button, or dragging a box aroundthem. Press the Color button on the color zone dialog to colorportions of the surface within the specified distance.
The image shows part of the phage T4 tail assembly. Regions of the EMdensity map near three structural proteins GP8, GP9, and GP11 are coloredblue, green and cyan.(EM database entry1089,and PDB model 1tja.)
Radial coloring | (August 2005, version 1.2154, details) |
| Higher contour level |
Surfaces can be colored according to radial distance. Use menu entry
Tools / Volume Data / Surface Color
to show the surface color dialog. Choose from the menu Usingelectrostatic potential, or other volume data, or by distance tocolor byRadius. To use radii ranging from the minimum to maximumradius for the surface press the Set full range colormap valuesbutton, then press the Color button at the bottom of the dialogto color the surface. The colors and radii can be changed and pressingthe Color button again will update the coloring. The Originentry field specifies where the radius is measured from.
The image shows a fibered phi29 virus particle colored red near the centerand blue near the extremities.(EM database entry1116.)
Electrostatic potential | (August 2005, version 1.2154, details) |
The image shows a solvent excluded molecular surface colored accordingto electrostatic potential. Blue represents positive potential andred negative. Zero potential is white, partially transparent.Chimera does not compute electrostatic potential, but can displayelectrostatic potential grid data computed by other programs (eg. DelPhi,APBS, UHBD).
To color a molecular surface open the molecular model(PDB 2sodin this image) and use menu entry
Actions / Surface / show
display the molecular surface. Use menu entry
Tools / Surface+Binding Analysis / Electrostatic Surface Coloring.
Clickthe Browse... button on the dialog that pops up and select theelectrostatic grid file (sod.phi for this image). Then press theColor button.
Color by density value | (August 2005, version 1.2154, details) |
A clipped and capped surface can be colored according to density map valuesusing
Tools / Volume Data / Surface Color
A surface coloring dialog is shown.Press the Set full range colormap values button to fill in densityvalues for a rainbow coloring spanning the range of density values foundon the surface. Turn on the Only color sliced surface face switchif desired, and then press Color. The coloring will update wheneverthe clip plane position or surfacing threshold changes.
A map of GroEL is shown, sliced perpendicular to the cylinder axis(EM database entry 1080).Red is low density and blue is high density.
Morph map | (October 2007, version 1.2456, details) |
To linearly pointwise interpolate from one map to another use the morphmap tool, menu entry
Tools / Volume Data / Morph Map
Choose the two maps and then move the Fraction slider tolinearly interpolate between them, 0 corresponding to the first map,and 1 correpsonding to the second map. The interpolated map is shownin the volume dialog and the graphics window with settings initiallymatching those of the first map. Threshold levels and colors for theinterpolated map can be changed in the volume dialog. The Playbutton gradually increases the interpolation factor to show a smoothanimation between maps. The Record button can record this to amovie file.
This tool makes the differences between related maps visually evidentbut is not a reliable guide to how the structuresundergo conformational changes. The example shows morphing between twoRNA polymerase II conformations (EMDB1283and1284).
Ambient Occlusion Lighting | (October 2007, version 1.2454, gaussian andsurface colordetails) |
Contour surfaces with recesses can be made to look more 3-dimensional bydarkening the recessed areas. If light cannot reach a deep pocket it shouldappear dark. The most direct way to achieve this is to shine lights onthe surface from many directions and compute shadows. Chimera only has twolights and does not currently compute shadows. In some cases the sameeffect can be achieved using the Surface Color and Gaussian Filter toolsas follows.
Use the Gaussian Filter tool, menu entry,
Tools / Volume Data / Gaussian Filter
to make a smoothed copy of the volume. Choose a Gaussian width aboutequal to the size of the recesses in the structure so the smoothedversion is a featureless blob. Then use the Surface Color tool
Tools / Volume Data / Surface Color
to color the original volume using the smoothed volume values. Choosetwo colors, press the Set full range colormap values button,make the color with lower value light (e.g. white) and higher valuedark (e.g. black). Then press the Color button. The smallervalues in the Gaussian smoothed map are the outer parts of theoriginal map while the larger values will be in recesses. Adjust the lowerand upper data values and press theColor button to achieve the desired degree of shading.
The image shown is a Trypanosoma 80S ribosome(EMDB1303).Silhouette edges (menu entry Tools / Viewing Controls / Effects) andreduced shininess (menu entry Tools / Viewing Controls / Shininess)have been used to increase the ambient occlusion depth effect.
Box face capping | (October 2007, version 1.2455, details) |
When a contour surface reaches the edge of the volume box the datavalues on the box faces that are higher than the contour level arecovered with a flat surface coincident with the box face. Thesepatches are not strictly contour surfaces since they pass throughdata values higher than the contour level.
This box face capping option is enabled by default and makes thecontour surface appear solid having no holes. To turn off the facecapping use volume dialog menu entry:
Features / Surface and Mesh Options
and switch off
Cap high values at box faces
Box face capping is usually preferable toplacing zeros on the boundaryof the data set because it gives perfectly flat surfaces, and workswhen showing different subregions of a volume data set.
Square mesh | (May 2006, version 1.2238, details) |
The default volume mesh display style shows a triangular mesh. To showjust the contour lines in the xy, yz and xz grid planes use volume dialogmenu entry
Features / Surface and Mesh Options
And turn on the Square mesh option. The mesh is then lessopaque and the square mesh grid shows the grid plane spacing. Using atransparent mesh color is also helpful for seeing atomic models fitinto a density map. You can make square meshes the default for futureChimera sessions using volume dialog menu entry
Features / Save default dialog settings
You probably want to close the surface and mesh options panel beforesaving the default settings since the currently displayed panels arealso saved as the defaults.
Close boundary holes | (November 2005, version 1.2186, details) |
| Boundary zero. | Holes, unlit interior. | Holes, lit interior. |
When high density extends to the boundary a data set the contoursurface shows a hole, and the inside of the surface is visible. Settingthe map values on the boundary of the data set to zero eliminates theholes. This is done with keyboard accelerator zb. Keyboardaccelerators are turned off by default. To activate them use menuentry
Tools / General Controls / Accelerators On
Then type zb in the graphics window to zero the volume data values on the6 faces of the data set currently shown in the volume viewer dialog.A new writable copy of the data is created which can be saved to a newfile using the volume viewer dialog menu entry File / Save Map As....
Closing the boundary holes is needed when computing thevolume enclosed by surfaces, and to makecapping of surfaces cut with clip planes work.It is also desirable to avoid visually confusing views of the interiorof the surface. An alternative to improve appearance is to make theinside of the surface dark by turning off theTwo-sided surface lighting option in the volume viewer dialog(menu entry Features / Surface and Mesh options).
The images show Paramecium Bursaria Chlorella Virus(PBCV-1)from the VIPERdb web site.
Smoothing surfaces | (August 2005, version 1.2154, details) |
The level of detail can be controlled by changing the Stepsetting near the top of the volume viewer dialog (menu entry Tools /Volume Data / Volume Viewer). A step setting of 2 2 2 meansevery other plane is used along the x, y and z axes of the data.A step of 1 1 1 uses all the data and shows the most detail.
You can additionally smooth the surface. This keeps the level of detailthe same but reduces sharp edges and faceted appearance of the surface.This is in the Options panel of the volume viewer dialog. Checkthe Options button at the top of the dialog to expand a long listof options. At the bottom of the list turn onSurface smoothing iterations. This moves each vertex of thesurface (which is made up of many triangles) towards the average position ofadjoining vertices. Two parameters control the degree of smoothing.The fraction of the distance to move a vertex towards the average isone parameter, and the other is the number of times to repeat the smoothing.
The image shows a machine that regulates fusion of vesicles with membranes,N-ethyl maleimide sensitive factor (NSF).(EM database entry 1059).It has been colored by cylinder radius using theSurface Colortool. Two copies of the data set are shown with step 1 1 1 on theleft and step 4 4 4 on the right, and smoothing turned on for both.
Multiple contour levels | (August 2005, version 1.2154, details) |
More than one contour level can be displayed. In the volume dialog(menu entry Tools / Volume Data / Volume Viewer) hold the ctrlkey and click on the histogram to add a contour level. To see the nestedsurfaces color them distinctly and use transparency or mesh display style.To color a level, click its vertical bar on the histogram and then clickon the square color button below the histogram. This shows the Colordialog. Press the Opacity button on the color dialog showsan additional slider labeled A that makes it possible to see throughthe surface.
The image shows 3 contour levels of the tail assembly of phage P22.(EM database entry1119.)
Display styles | (August 2005, version 1.2154, details) |
Volume data can be displayed in 3 styles: contour surfaces, meshes, or solidstyle. There are checkbuttons on the volume dialog for the 3 styles.Mesh and surface are the same except that mesh just shows the edges ofthe triangles composing the surface. Solid style assigns a degree oftransparency to every grid point in the volume and then displays the fullsemi-translucent data.
The image shows a potassium channel(EM database entry 1094)with halfthe tetramer as a red surface, a quarter as a blue mesh, and a quarter asa yellow solid rendering. To display the 3 different styles at the sametime I opened 3 copies of the data and cropped each to show just part of thechannel.
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