Chimera Images

[Osman Briseno]

Chimera performs offscreen rendering as permitted by the system.Offscreen rendering is not supported bycertain older machines. On those systems,the image will be redrawn in the graphics window, piece by piecedepending on the specified image size and degree of supersampling; during this process,the graphics window should not be obscured by other windows or moved offscreen, even partially.

The following tips mainly apply to high-quality rendering directly in Chimera. Images rendered in Chimera are often clearer and more illustrative than thosemade with the (noninteractive) raytracing option,and can even include shadows.

Background color is set to white by thepublication presets mentioned above, but can be set to any colorwith the Color Actions dialog,the background command, orthe Background preferences.The latter two can also set the background to a gradient of multiple colors or to an image read from a file.If system hardware permits, images can be saved with a transparent background.

Silhouettesare outlines that emphasize borders and discontinuities.Although shown in the interactive display, these are mainly intended for output images, as supersampling makes them look much smoother in the image than on the screen.Whether silhouettes are shown and their linewidth and color can be controlledwith the Effects tool orthe set command.Publication presets #1 and #2 turn on silhouettes and turn off depth cueing.Silhouettes can also be combined with depth cueing,as in publication preset #5.This silhouettes setting is global (applies to all models),but when it is on, the silhouettes for an individual model can be toggledwith the command setattr,the Selection Inspector,or the molecule model attributes panel.If outlines are desired but the silhouettes seem to highlight too many contours,a trick is to use the selection outline instead,as it is limited to the perimeters of selected objects.The selection outline color can be changed, e.g to black, in the Selection preferences.Although the linewidth is not adjustable, a thicker line relative to theselected object(s) can be obtained by resizing the graphics window smaller; a large output image can still be obtained by specifying larger dimensions when saving the image.

Smoothnesscan be increased by increasing the pixel dimensionsof an image (its resolution). Additionally, independent of resolution:

• Atoms, bonds, ribbons.Display styles other than wire (which is not recommended for publication images)can be smoothed by raising the subdivision levelwith the Effects tool orthe set command.This setting also affects curved geometric objectsdefined in BILD format.The publication presets increase subdivision to 5.0 if the current value is lower.
  
  
• Surfaces. The smoothness of amolecular surfacecan be increased by increasing its vertex densitywith the command setattr,the Selection Inspector, or the molecular surface attributes panel(see also the New Surfacespreferences). This parameter can also be specified when asurface is displayed with the surfacecommand. The publication presetsraise vertex density to 10.0 for any existing molecular surfaceswith lower values. Separate smoothing options are available inMultiscale Models andVolume Viewer for the surfaces they create(see also the command sop smooth).
  
  
• Supersampling.The smoothness of edges in saved images can be increased by supersampling,where Chimera automatically saves an image at higher resolution (largerpixel dimensions) than requested and then samples it back down to the requested final size. The default level of supersampling, 3x3, isusually recommended for publication images and gives much smoother edges than no supersampling (1x1). For individual images, the supersampling levelis specified in the Save Image dialogor with the copycommand's supersample keyword.The command movie recordand dialogs for recording moviesalso include supersampling options.Supersampling increases calculation time with little effect on file size.A potential disadvantage of supersampling is that linessuch as silhouettesor hydrogen-bond representationsmay become unexpectedly thin in the final image because there is asystem-dependent limit to how wide they can be drawn in the initial image.The File... Save Image dialog reports the effective maximum linewidthgiven the current supersampling level and image size.It may be possible to achieve the desired linewidth by reducing the supersampling level and/or the pixel dimensions of the image.

Ribbon path. By default, the ribbon path is a smoothed splinethat may deviate from the true positions of the backbone atoms, making bonds to sidechains appear unnaturally short or long(details...).The path calculation can be adjusted with the commandribspline,the molecule model attributes panel,and the Selection Inspector.For proteins,a cardinal spline without smoothing is constrained to pass throughα-carbon coordinates, but gives a very rumpled ribbon;a cardinal spline with strand-only smoothing may be a useful compromise(e.g.,ribspline cardinal smooth strand).

Clipping planes cut away portions of structures, surfaces and objects.The global clipping planesshown in the Side Viewaffect all models and can only be perpendicular to the line of sight. In addition, each model can have aper-model clipping planeoriented at any angle.Surface Capping controls whether clipped surfaces appear solid or hollow.

Color space. Some publications require images to be in the CMYK color space.Chimera currently saves images in only the RGB color space, soa separate application such as Adobe Photoshopmust be used to switch between the two.

Choosing colors.Several factors should be considered in choosing colors, includingwhat the colors are meant to indicate, their distinguishability fromeach other and from the background,and whether viewers may have color vision deficiencies.Useful websites include:

• ColorBrewer- multipurpose color-scheme picker; 3- to 12-color schemes are displayed on a map and rated by suitability for red-green colorblind viewers,printing, and/or photocopying. The HEX color specifications at this siteare Tk codes,which can be used as color names in many Chimera commandsand in the Color Editor.
• Vischeck- simulates the effects of color-blindness on your own uploaded imageor a specified web page

See also: Color Editor,Palette Editor

Deploying philosophical and ethnographic theory, Severi unfolds new approaches to research in the anthropology of ritual and memory, ultimately building a new theory of imagination and an original anthropology of thought. This English-language edition, beautifully translated by Janet Lloyd and complete with a foreword by David Graeber, will spark widespread debate and be heralded as an instant classic for anthropologists, historians, and philosophers.

The translation of The Chimera Principle: An Anthropology of Memory and Imagination is a major event in Anglo-American anthropology. Remarkable for its scholarly depth, its ability to recast the whole field of memory and imagination through its relation to visual and sound images, and above all its complete mastery over comparative ethnography, this book is a stunning landmark in anthropological theory.

In The chimera principle, Carlo Severi has done nothing less than to pioneer an innovative anthropology of memory, opening up areas of inquiry from which everyone throughout the humanities and the social sciences will learn.

The contents of the Chimera graphics windowor a raytraced image from POV-Ray can be saved to a file with File... Save Image.See also: copy,making movies, exporting a scene, tips on preparing images

When Maintain current aspect ratio is on, the image width/height ratio is constrained to match the width/height ratio of the graphics window (not including borders). Entering the width automatically adjusts the height and vice versa.

When Maintain current aspect ratio is off, both width and height can be set as desired. Grow to Fit resizes the graphics window to match the image aspect ratio by increasing one window dimension (i.e., width or height), while Shrink to Fit resizes the graphics window to match the image aspect ratio by decreasing one window dimension. If the window has not been grown or shrunk to match the image aspect ratio, a saved image will include more than what is displayed.

When dimensions are specified in units of length (anything other than pixels), they are converted to inches internally and multiplied by the Print resolution (dpi) to give the output pixel dimensions. The print resolution setting is saved in the preferences file.

After the image has been redrawn, the file name and type (format) can be specified, or the save can be canceled. Images can be saved in the PNG, TIFF, JPEG, PS (PostScript), andEPS (Encapsulated PostScript) formats. The quality of JPEG filescan be specified as an integer in the range 5-95,with higher values corresponding to higher quality and larger files.

Additional format options for stereo pairsare stereo JPEG (*.jps) and stereo PNG (*.pns).Viewing such files as standard JPEG and PNG shows side-by-side images, but special viewers are available to show them as stereo.Free viewers includeStereoPhoto Maker,JPSViewer LE, and NVidia's consumer3D stereo driver (requires the appropriate graphics hardware).

Presets are predefined combinations of display settings. Choosingan entry in the Presets menuapplies its settings. Further changes can be made as desired after a preset has been applied.Publication presets make the background white, adjust display styles,and increase the smoothness of curved objects (which may decrease interactiveperformance).

c80f0f1006