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Chimera 1.9

Sequence Viewer

The Multalign Viewer tool displays individual sequences and multiple sequence alignments. Sequence alignments can be read from external files (several formats) or created by other tools in Chimera. Structures opened in Chimera are automatically associated with sufficiently similar sequences in the alignment. After association,
• mousing over a residue in the sequence shows its structure residue number
• selecting in the sequence selects residues in the structure(s) and vice versa
• structures can be superimposed using the sequence alignment
Various measures of sequence conservation and structural variation (RMSD) can be computed and shown above the sequences as histograms, and on the structures with color or worm radius. Secondary structure elements can be depicted as colored boxes or regions on the alignment. Regions can also be created by hand.

Morphing

Different conformations and even different proteins can be compared by morphing from one structure to another. Users can specify the method of coordinate interpolation and how many intermediate structures should be generated. The result is displayed in Chimera`s trajectory viewer, MD Movie. The morph can then be saved in coordinate form or recorded as an animation.

Morphing

Different conformations and even different proteins can be compared by morphing from one structure to another. Users can specify the method of coordinate interpolation and how many intermediate structures should be generated. The result is displayed in Chimera`s trajectory viewer, MD Movie. The morph can then be saved in coordinate form or recorded as an animation.

Chemical Knowledge

* determination of atom types in arbitrary molecules, including non-standard residues
* ability to add hydrogen atoms
* high-quality hydrogen bond identification
* selection of atoms/bonds by element, atom type, functional group, amino acid category
* interactive bond rotation, distance and angle measurements

Showing ConSurf Results

The ConSurf Server provides results as Chimera Web data; after browser configuration, a single click displays the color-coded query structure and multiple sequence alignment with phylogenetic tree and custom headers in a locally installed copy of Chimera (details).

Special thanks to Elana Erez and the Ben-Tal and Pupko groups at Tel Aviv University, and to Fabian Glaser at the Technion.

Volume Data

Chimera`s Volume Viewer displays three-dimensional electron and light microscope data, X-ray density maps, electrostatic potential and other volumetric data. Contour surfaces, meshes and volumetric display styles are provided and thresholds can be changed interactively. Maps can be colored, sliced, segmented, and modifications can be saved. Markers can be placed and structures can be traced. The accompanying image shows a density map of Kelp fly virus from electron microscopy colored radially and with an octant cut out.

Multiscale Models

The Multiscale Models extension allows Chimera to display large complexes such as virus capsids, ribosomes, and chromatin. It displays the quaternary structure of PDB models and allows subunits to be selected and shown in atomic detail. Matrices are read from PDB files that specify the biological unit. Crystallographic packing can also be shown.

Screening Docked Molecules
View Dock image

The program DOCK calculates possible binding orientations, given the structures of "ligand" and "receptor" molecules. Typically, a large database of small molecule structures is searched for compounds that may bind the receptor. The Chimera extension ViewDock facilitates interactive selection of promising compounds from the output of DOCK. The molecules can be viewed in the context of the binding site and optionally, screened by number of hydrogen bonds to the receptor. The Dock Prep extension prepares a receptor for input to a docking program by adding hydrogens, assigning partial charges, and performing other related tasks.

User-Driven Analysis

Users can easily import structure-related data into Chimera in the form of attributes, or values associated with atoms, residues, or models. The data can be imported with Define Attribute and then represented visually with color ranges, atomic radii, or "worm" thickness. Such data can also be manipulated programmatically in Chimera, and in fact Chimera was designed with extensibility and programmability in mind. It is largely implemented in Python, with certain features coded in C++ for efficiency. Python is an easy-to-learn interpreted language with object-oriented features. All of Chimera`s functionality is accessible through Python and users can implement their own algorithms and extensions without any Chimera code changes, so any such custom extensions will continue to work across Chimera releases. Many programming examples are provided to assist extension writers.

Rotamers

Amino acid sidechains adopt different conformational states, or rotamers. Rotamers from the Dunbrack backbone-dependent library or the Richardson "penultimate" library can be viewed, evaluated, and incorporated into structures with the Rotamers tool. A residue can be changed into a different conformation of the same type of amino acid or mutated into a different type. Rotamer torsion angles and library probability values are listed in a dialog, along with (optionally) hydrogen bonds, clashes, and agreement with electron density data. Only rotamers chosen in the list are displayed. When a single rotamer is chosen, it can be incorporated into the structure. The image includes 2D labels.

Morphing Density Maps

Related density maps can be compared by morphing from one to the other. Several intermediate maps are generated by interpolating between the starting and ending maps. The morph can be viewed interactively and recorded as a movie. The contour level can be adjusted automatically to keep the enclosed volume constant throughout the morph, and other aspects of map display can be adjusted with Volume Viewer.

Volume Plane Display

Volume data can be shown a single plane (or slab) at a time with the Planes feature in Volume Viewer. Plane display can be set to oscillate along the data X, Y, or Z axis, or the plane location can be specified interactively with a slider.

(More features...)

volume plane topography
Topography

Values in a plane of volume data can be shown as heights normal to the plane (a topographic map). When a single plane is displayed with Volume Viewer, the command topography will plot the values as heights in a surface.

(More features...)

surface color by density
Coloring by Density

A surface can be colored by density or other volume data. In the image, the surface is clipped and capped, and only the cap is colored by density. Different coloring schemes can be applied.

(More features...)

radial surface color
Radial Coloring

A surface can be colored radially, that is, by distance from a user-specified point. Additional options include coloring by distance from an axis or a plane. Different coloring schemes can be applied.

(More features...)

ribbon color by conservation
Coloring by Conservation

A structure can be colored to show values of an attribute such as residue conservation. Opening a sequence alignment in Chimera automatically displays it in Multalign Viewer and associates it with any similar structures (a few residue mismatches are allowed). A variety of conservation measures can be computed. The image was created using the PFAM Carb_anhydrase seed alignment PF00194_seed.slx and includes a color key and 2D labels.

CASTp Pocket Data

Structures and their pocket measurements can be fetched directly from the Computed Atlas of Surface Topography of proteins (CASTp) database or read from local files previously returned by the CASTp server. In Chimera, the pockets and their measurements are shown in a pocket list. Choosing one or more pockets from the list performs actions on the structure, such as zooming in on a pocket, showing its surface, and/or selecting the atoms around it.
The figure shows the four largest pockets by volume identified by CASTp for PDB entry 1ovh, a cavity mutant of T4 lysozyme. The pocket surfaces are colored yellow, orange, pink, and magenta in order of decreasing volume. The largest (yellow) is lysozyme`s active site, with two openings. The second largest (orange) is the engineered cavity, completely enclosing a bound aniline derivative. The mutated positions are shown in red. Chloride ions are displayed as green balls.

Density Display

Electron density maps can be displayed as mesh or solid isosurfaces with Volume Viewer. Contour levels can be adjusted interactively, multiple levels can be shown for a given map, and display can be restricted to a zone around specified atoms. The image (see how-to) shows PDB entry 2fma and its electron density map. Chimera can fetch the map directly from the Electron Density Server.

B-Factor Coloring

A structure can be colored to show values of an attribute such as atomic B-factor. The image includes a molecular surface that has been clipped and capped, 2D labels, and a color key. Color Zone was used to color the planar cross-section of the surface (see image how-to).

Structure-Based Sequence Alignment

Given two or more superimposed structures, Match→Align creates a corresponding sequence alignment. The user specifies a distance cutoff for residues allowed to be in the same column of the output alignment. In proteins, the distances are measured between α-carbons. The method is independent of residue types and how the structures were superimposed.
The figure shows a superposition from MatchMaker of five proteins from the SCOP WD40 superfamily and a corresponding sequence alignment from Match→Align, automatically shown in Multalign Viewer. In the sequence alignment, light green and yellow boxes indicate strands and helices, while the headers RMSD and Conservation show spatial and sequence conservation, respectively.

Superimposing Structures

There Are Several Ways To Superimpose Structures In Chimera:

• MatchMaker performs a fit after automatically identifying which residues should be paired. Pairing uses both sequence and secondary structure, allowing similar structures to be superimposed even when their sequence similarity is low to undetectable.
The figure shows five distantly related proteins (pairwise sequence identities

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| Visualization | Trajectories | Supramolecular Assemblies | Sequence Alignments | Molecular Structures | Docking Results | Density Maps | Conformational Ensembles |

History updates (Complete changelogs since the listing on this site)

1.9 [04-25-14]

General Changes:
  • optional icon to show and control menu selection mode (Append, Intersect, Replace, or Subtract)
  • some Preferences reorganization, including new categories: Labels, Selection
  • model silhouette attribute allows showing silhouettes for specific models (previously all or none)
  • Ramachandran Plot probabilities can be assigned as a residue attribute
  • new output movie format WMV2
  • new input volume format VTK structured points, ASCII
  • new export formats COLLADA, VTK
  • more efficient save/restore of coordinates in session files (for MD trajectories or very large structures, ~5% smaller session files and 3X faster save/restore)
New Tools:
  • Align Chain Sequences (Sequence) — generate a multiple sequence alignment (MSA) of structure chains using a Clustal Omega or MUSCLE web service hosted by the UCSF RBVI
Tool Changes:
  • APBS (Surface/Binding Analysis) — by default, explicit solvent is omitted from the calculation
  • Axes/Planes/Centroids (Structure Analysis) —
    • axis, plane, and centroid objects are now surface models (improved behavior with transparency and shadows; can be recolored with Actions menu, color, scolor)
    • axes can be calculated from centroids as well as atoms
  • Build Structure (Structure Editing) —
    • can build nucleic acid double helices
    • join models (peptide bond option) allows specifying new φ angle
    • button to delete selected atoms/bonds
  • Color Key (Utilities) — tick mark length and width settings added
  • Distances (Structure Analysis) — default distance monitor color, linewidth, and line style can be saved to preferences
  • Find Clashes/Contacts (Structure Analysis, Surface/Binding Analysis) — option to display contact residues if not already shown
  • Icosahedron Surface (Higher-Order Structure) — added line-width setting for mesh
  • MD Movie (MD/Ensemble Analysis) —
    • separate settings for including or omitting alkali metal ions, other metal ions, and monatomic anions from various calculations (RMSD, clustering, averaging)
    • sessions support partly loaded trajectories
  • Minimize Structure (Structure Editing) —
    • default number of conjugate gradient steps decreased from 100 to 10
    • improved logging
  • Morph Conformations (Structure Comparison) — chain pairing uses chain IDs if the sets of IDs are identical
  • Morph Map (Volume Data) — optionally interpolates colors if the maps have the same number of coloring thresholds
  • Multalign Viewer (Sequence) —
    • sequence names can be edited
    • regular expression searching
    • protein sequences with U (selenocysteine), O (pyrrolysine) can be aligned
    • Clustal Omega or MUSCLE can be used via web service to realign the sequences
    • active region contents can be opened in a new window
  • Multiscale Models (Higher-Order Structure) — surfaces of different chains with the same sequence are colored alike
  • Rotamers (Structure Editing) — added Dynameomics rotamer library
New Commands:
  • adjust — change bond angle or bond length
  • colorkey — command-line implementation of the Color Key tool, plus direct specification of color key placement
  • leap — use a Leap Motion Controller with Chimera
  • mda — BLAST-search and retrieve structures related to a query sequence, lay them out left→right in Chimera by N→C matches to the query
  • struts — add pseudobonds to a molecule to strengthen it for 3D printing
Command Changes:
  • angle — option to report angle between 1-2 and 3-4 vectors instead of 1-2-3-4 dihedral
  • apbs
    • by default, explicit solvent is omitted from the calculation
    • added options to use a local executable or an alternative Opal web service
  • coulombic — atoms/charges to use can be specified independently of the surface to color; this allows coloring the surface of one molecule by the potential from another, for example, or coloring nonmolecular surfaces such as density isosurfaces
  • define
    • axis, plane, and centroid objects are now surface models (improved behavior with transparency and shadows; can be recolored with Actions menu, color, scolor)
    • axes can be calculated from centroids as well as atoms
  • findclash — option to reveal (display) contact residues if not already shown
  • matrixcopy — allows many-to-many transformation copying (previously just one-to-one or one-to-many)
  • minimize — default number of conjugate gradient steps decreased from 100 to 10; improved logging
  • morph — chain pairing uses chain IDs if the sets of IDs are identical
  • pdb2pqr — added options to use a local executable or an alternative Opal web service
  • ramachandran (undocumented in earlier versions) — can assign probabilities as a residue attribute
  • reset
    • options such as holdSteady can be used with the default position
    • moveModels can be used without holdSteady
  • set — can enable/disable transparent background for subsequently saved images
  • swapaa — added Dynameomics rotamer library
  • vina — added options to use a local executable or an alternative Opal web service
  • volume — added options to automatically set threshold (contour) level so that the surface encloses a target spatial volume
  • vop
    • vop morph optionally interpolates colors if the maps have the same number of coloring thresholds
    • vop maximum (new) takes pointwise maximum of input maps
    • vop multiply (new) multiplies maps, for example to apply a mask
  • vseries — added options to open and close volume series, jump playback to a specific frame, perform various types of processing such as alignment, normalization, cropping, and compression, and save to file in Chimera map format
Notable Bugfixes:
  • Write Prmtop now works when using newer force fields
  • Chimera menus and dialogs use system font size settings (tested mainly on Linux)
  • Fixed bounding box calculation for transformed VRML nodes so that when exported VRML files are read back in, they rotate correctly
  • Fixed problem with “missing structure” loop modeling that allowed an extra residue at the C-terminal end of the modeled part to move
  • Fixed locking bug in suppport for "chimera --send"
Known Bugs:
  • surfaces fail for some structures
  • crash on Mac dual display systems. Details.

Other versions : 1.8 1.7 1.6.2 1.6 1.5.3 1.5.2 1.5.1 1.5 1.4.1

v1.8 [04-29-13]

General Changes:

  • “connected fragment” inserted into selection cascade between residue and chain
  • SMILES-to-3D uses the translator at cactus.nci.nih.gov if the smi23d service does not produce a result
  • session notes and thumbnail can be saved via File... Save Session As... and later viewed by clicking the session filename in the Restore Session dialog (previously session notes could only be seen/edited in Notepad)
  • items can be deleted from the recent data list in Rapid Access
  • duplicate consecutive commands can be removed from the command history
  • new volume input format, Amira mesh (scalar)
  • new 3D object input format, AutoPack results
  • support added for Rich Molecular Format, including an interface for exploring the contents
  • support added for Gromacs 4.6 trajectories
  • quit-Chimera confirmation default “conditional” instead of “always” (General preferences)
  • Mac multi-touch trackpad support (General preferences)
  • more efficient use of memory by multi-copy multiscale surfaces
  • REST interface (see New Tools)
New Tools:
  • RESTServer (Utilities) — allow communication with Chimera through REST interface
Tool Changes:
  • 2D Labels (Utilities) — existing arrows can be repositioned
  • Find Clashes/Contacts (Structure Analysis, Surface/Binding Analysis) — intramolecular interactions can be excluded, where a molecule is defined as a covalently bonded set of atoms
  • FindHBond (Structure Analysis, Surface/Binding Analysis) — intramolecular and/or intraresidue H-bonds can be excluded
New Commands:
  • apbs — command-line implementation of APBS interface
  • pdb2pqr — command-line implementation of PDB2PQR interface
  • rna — build rough but potentially large-scale models of RNA and DNA
  • vina — command-line implementation of AutoDock Vina interface
  • vseries — display an ordered sequence of volume data sets (command implementation of Volume Series)
Command Changes:
  • 2dlabels — existing arrows can be repositioned (achange start/end options)
  • colordef — option to list all user-defined color names
  • findclash — intramolecular interactions can be excluded, where a molecule is defined as a covalently bonded set of atoms
  • findhbond — intramolecular and/or intraresidue H-bonds can be excluded
  • getcrd — can report transformed coordinates
  • mask
    • modelId option to specify model number of output map
    • extend option to specify padding in grid units
  • measure
    • fieldLines to show electric field lines for potential maps
    • mapStats to calculate map mean, standard deviation from mean, and RMS deviation from zero (command implementation of Volume Mean, SD, RMS)
    • mapSum to sum map values above a specified threshold
  • ~namesel to “forget” a previously named selection
  • reset — options allow partially restoring a position (can keep the viewpoint fixed on one model and move only a subset of the others)
  • sop
    • split to split disconnected parts of a surface into independently selectable pieces
  • split — can split a model based on ligands, bonded sets of atoms, etc. (formerly just chains)
  • surface — probe radius, vertex density, and whether to calculate multiple components can be specified directly in the command
  • vop
    • threshold to reassign values that are below a specified minimum and/or above a specified maximum
    • localCorrelationsubtractMean option to subtract the local mean before calculating each correlation value
Notable Bugfixes:
  • Animation mouse drag uses left mouse button instead of middle
  • Animation supports custom surface colorings
  • Animation works with volume isosurfaces
  • Autodock Vina prep scripts check for receptor and ligand hydrogens, add them if missing (previously no hydrogens were added if the user chose not to add hydrogens with Chimera)
  • ViewDock correctly reads mol2 files again
  • Fixed export for bond cylinders that were parallel to the Y-axis
Known Bugs:
  • surfaces fail for some structures
  • Nvidia Quadro graphics on Windows 7 cause ten-second freezes when picking atoms (Ctrl-mouseclick) of large models (20000 atoms). This is caused by the graphics driver "adaptive" power management setting. Using Nvidia Control Panel, Manage 3-D Settings, Global Settings tab to change Power Management to "Prefer maximum performance" solves this problem. Bug report #11315.

v1.7 [12-20-12]

General Changes:

  • AmberTools updated to version 12 (new force field, etc.)
  • cleaner CASTp pocket display, disconnected fragments hidden automatically
  • “show distances to nearby residues” function added to atom context menu (raised by doubleclick-select)
  • “click to center” mouse mode added (default Ctrl-3, can reassign in Mouse preferences)
  • publication presets no longer change atom/bond display styles (except wire → stick)
  • presets can be user-defined (Chimera command or Python file locations specified in Presets preferences)
  • Actions... Color menu works on axis, plane, centroid objects
  • Image Save dialog reorganized, integrated with output file specification
  • Fetch by ID allows entering multiple IDs for same database
  • new input format: STL
  • Movie preferences removed, settings put back into various recording dialogs
  • new movie formats (output): H.264, VP8/WebM, Theora
  • default lighting changed
  • interactive shadows faster, available on more systems, quality adjustable in Effects
  • faster loading of large molecules
  • faster graphics for large molecules on many systems
  • default maximum graphics frame rate doubled, to 60 fps
  • smoother rotation with mouse drag
  • Mac retina display full-resolution used for graphics and text
  • new pseudobond style: spring
  • rounded ribbons look flatter (actually a bugfix; incorrect highlighting had given the illusion of plumpness)
New Tools:
  • APBS (Surface/Binding Analysis) — interface to Poisson-Boltzmann electrostatics calculations with APBS, using either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy
  • AutoDock Vina (Surface/Binding Analysis) — interface to single-ligand docking with AutoDock Vina, using either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy
  • Model/Refine Loops (Structure Editing) — interface to Modeller for building missing parts or refining existing parts (the former Model Loops tool only performed the latter and did not facilitate combining the refined and unchanged parts)
  • Notepad (Utilities) — allows entering descriptive text that can be saved along with sessions
  • PDB2PQR (Structure Editing) — interface to structure cleanup and charge/radius assignment with PDB2PQR, using either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy
Tool Changes:
  • 2D Labels (Utilities) —
    • labels can have backgrounds (colored rectangles underneath the text)
    • buttons added to hide/show all 2D labels or arrows
  • Add Charge (Structure Editing) — force field options changed, new default: Amber ff12SB
  • Animation (Utilities) —
    • timeline for arranging scenes, playing/recording animation
  • Blast Protein (Sequence) — results table can be exported as comma-separated values
  • Build Structure (Structure Editing) —
    • can add atom at specified X,Y,Z coordinates
    • bond length adjustment slider and revert button
    • new section for adjusting bond (valence) angles
    • Adjust Torsions moved to this tool (was previously part of Structure Measurements)
  • Effects (Viewing Controls) —
    • transparent background setting moved to Save Image dialog
    • local viewer option removed
    • new settings related to shadows and transparency
  • Ensemble Cluster (MD/Ensemble Analysis) — clustering information can be saved to a text file
  • Hide Dust (Volume Data) — surface area, area rank, and volume rank added as metrics
  • Lighting (Viewing Controls) —
    • for better control, contrast split into two parameters: contrast and key-fill ratio
    • quality setting removed (former “glossy” is new default)
  • MD Movie (MD/Ensemble Analysis) —
    • can calculate average structures for specified frame ranges or clusters
    • can plot RMSD (relative to a single reference frame) vs. frame number
    • GROMACS .xtc (compressed) trajectory files supported, faster reading of .trr trajectory files courtesy of XTC Library
    • input as multiple PDB or XYZ files no longer requires consecutive numbering in filenames (skipped numbers OK)
    • occupancy calculation can treat atoms as VDW spheres, incrementing all grid cells containing part of an atom (previously could only treat atoms as points, the current default)
    • clustering information can be saved to a text file
  • Minimize Structure (Structure Editing) — uses force field parameters concordant with charges for Amber ff12SB, ff03.r1, ff99SB, or ff99bsc0 (previously always used ff99 parameters)
  • Model Loops removed, replaced with new tool Model/Refine Loops
  • Multalign Viewer (Sequence) —
    • allows using a subset of sequences as guides for adding a new sequence
    • Region Browser has menu for viewing different sets of regions, those for the entire alignment or those for an individual sequence (now that each sequence can have many UniProt feature annotations)
    • Region Browser shows Start, End of individual-sequence regions
  • PipesAndPlanks (Depiction) —
    • helix and strand directionality can be shown with arrows
    • distinct coloring per secondary structure element can be achieved by setting color wells to No Color (uses the ribbon color of the first residue per element)
    • significantly improved “joins” between coil, pipe, and plank representations
    • coil subdivision can be adjusted
    • edge color settings added to outline parts for which standard silhouette edges are not shown
  • ViewDock (Surface/Binding Analysis) — reads PDBQT format from AutoDock and AutoDock Vina, Mol2 format from GOLD
  • Volume Tracer (Volume Data) —
    • changes in mouse mode defaults: marker creation on planes and spots (local maxima) both turned on, automatic linking turned off
    • marker creation on spots applies to all volume displays (not just the active data set) and the slice graph includes all displays under the mouseclick
    • default marker/link color changed to yellow
  • Volume Viewer (Volume Data) —
    • changes in Planes including mouse mode for dragging planes
    • Orthogonal planes feature for viewing planes perpendicular to data axes, optionally as box faces
New Commands:
  • play — animate complex motions such as radial “explosion” of multiscale surfaces
  • transparency
    • set transparency of atoms, ribbons, etc. without otherwise changing their colors
    • can be applied gradually over a specified number of frames
Command Changes:
  • 2dlabels
    • labels can have backgrounds (colored rectangles underneath the text)
    • all 2D labels or arrows can be changed with a single command using * as name
  • addcharge — force field options changed, new default: Amber ff12SB
  • center — works on surface pieces (previously only atoms)
  • color
    • can color nonmolecular surface models
    • specifiers added for bond labels, bonds-only
  • coordset
    • multiple trajectories can be specified in the same command with a comma-separated list or range of model numbers
    • playback loop option
  • copy — can specify image dimensions in units of length, image dpi
  • fitmap
    • eachModel option to fit multiple models independently
    • listFits to show results in Fit List dialog
    • radius to restrict global search radius
  • lighting
    • for better control, contrast split into two parameters: contrast and key-fill ratio
    • changes in defaults, including glossy quality (former default renamed coarse)
  • mcopy — residue pairing can be user-specified (previously pairing required identical residue names, numbers, and chain IDs)
  • movie
    • several usability improvements (output format can be specified by filename suffix, etc.)
    • formats option to list the available movie formats
    • ignore option to start/stop ignoring movie commands, useful during script development
  • perframe
    • other commands can be embedded directly, not only as an alias
    • variables other than frame count can be substituted
    • allows execution at multi-frame intervals
  • preset — presets (including custom) can be specified by name
  • rock, roll, turn — default rotation per frame halved to compensate for doubled default frame rate (see General Changes)
  • roll, turnprecessionTilt to specify additionally rotating around a moving axis that is carried along by the main rotation
  • runscript — specifying the script as browse or browser calls up a dialog for locating/opening the file
  • set
    • keywords can be truncated, underscores removed
    • fieldOfView to adjust horizontal field of view angle
    • flatTransparency to make apparent transparency independent of the viewing angle
    • maxFrameRate to adjust maximum graphics frame rate
  • shape
    • boxpath - zigzag “beams” connecting a series of atoms
  • sop
    • hidePieces and showPieces to toggle display of specified surface pieces (independently selectable parts)
    • hideDust metrics added: surface area, area rank, volume rank
    • transform to scale, rotate, and shift surfaces
  • surfacevisiblePatches option to display only the N largest-area contiguous patches for cleaner display of pockets and other partial molecular surfaces
  • stereo — tilt angle can be specified for dome mode
  • volume
    • orthoplanes to display 2-3 orthogonal planes for the same dataset
    • boxFaces to display orthogonal planes as box faces
    • expandSinglePlane to expand a single plane along its axis to the full thickness of the data
  • vop
    • falloff to smooth boundaries of masked density
    • fourier to generate map of phase values (–π to π)
    • localCorrelation to calculate map-map correlation over a sliding box
    • new options to cover for using map symmetries and specifying unit cell dimensions
Notable Bugfixes:
  • Chimera-Modeller interface fixed to handle templates containing modified mainchain residues
  • independent rotation applies to hidden models
  • corrected single-layer transparency of VRML models (nucleotides, axis/plane/centroid representations, BILD objects)
  • shadows work with a single light and are ignored with ambient lighting
Known Bugs:
  • surfaces fail for some structures
  • Nvidia Quadro graphics on Windows 7 cause ten second freezes when picking atoms (ctrl mouse click) of large models (20000 atoms). This is caused by the graphics driver "adaptive" power management setting. Using Nvidia Control Panel, Manage 3-D Settings, Global Settings tab to change Power Management to "Prefer maximum performance" solves this problem. Bug report #11315.

v1.6.2 [07-10-12]

General Changes:

  • new Rapid Access interface to frequently used data and tools shown automatically upon startup, but can be hidden/shown at any time by clicking the lightning-bolt icon, or hidden by opening 3D data
  • new fetch type UniProt, protein sequence and annotations
  • default fetch directory set to ~/Downloads/Chimera (previously none) and option to ignore cached data added to Fetch by ID dialog
  • changed default model colors
  • labels drawn in front (default, Background preferences)
  • ribbon cardinal spline option for closer tracking of backbone atom positions, associated parameters for additional smoothing of strand and/or coil, ribbon “stiffness” (molecule model attributes, see also ribspline command)
  • global single-layer transparency, on by default in Effects (previously, single-layer transparency was per-surface and unavailable for ribbons and atoms; this individual surface attribute has been removed). Rendering only the topmost transparent layer simplifies the display and effectively de-emphasizes transparent parts.
  • the background can be set to a vertical multicolor gradient or to an image read from a file
  • Color Actions dialog includes "more..." buttons to show additional background and depth-cueing settings
  • PDB chain "molecule" info reported in Reply Log upon input, shown in status line when the cursor is paused over the chain
  • new residue attribute uniprotIndex (residue number in the corresponding UniProt sequence, determined from PDB header information using a web service provided by the RCSB PDB)
  • symmetry matrices read from mmCIF (previously only PDB)
  • new input/output type, spheres in the sphgen format used by DOCK
  • ViewDock reads Maestro docking output
  • new export type, WebGL (experimental feature)
  • CASTp —
    • pocket information saved in sessions
    • pocket surfaces optionally colored to show hydrophobicity
  • Save Image dialog includes option to save temporary session file
  • maximum image supersampling reduced from 6x6 to 4x4 because high levels increase computational demands without further visible improvement
  • changing the horizontal field of view camera parameter no longer changes the camera Z-position, and changing the width of the graphics window no longer changes either of those
  • saved positions include horizontal field of view value
  • new camera modes: dome, truncated dome
  • BILD/VRML text support added (see BILD .cmov and .font directives)
  • scaling with mouse scroll wheel and touchpad scrolling can be turned off (Mouse preferences)
New Tools:
  • Animation (Utilities) **under development, not fully functional, may change significantly** — save/restore Chimera scenes
  • Cage Builder (Higher-Order Structure) — create polyhedral cages composed of hexagons, pentagons, and other polygons
  • Change Chain IDs (Structure Editing)
  • MultiFit (Volume Data) — simultaneous rigid fitting of multiple structures into density (uses RBVI web server running the program MultiFit from the Sali lab)
  • Palette Editor (Utilities) — create and choose palettes (series of colors and interpolation method; currently used for background color gradients)
  • Renumber Residues (Structure Editing)
Tool Changes:
  • AddCharge (Structure Analysis, Structure Editing) — ATP, ADP, GTP, GDP now treated as standard residues (charge lookup from Amber parameter database, Bryce Group, Manchester)
  • AddH (Structure Editing) —
    • less common protonation states of Asp, Glu, Lys, Cys can be specified
    • new default is to consider each model in isolation, otherwise other models in the vicinity may affect hydrogen placement
  • Adjust Torsions (Structure Editing) — terminal bonds can be rotated
  • Blast Protein (Sequence) — many more columns of information can be shown for pdb hits (ligands, resolution, etc.)
  • Build Structure (Structure Editing) —
    • easier peptide linking with Join Models
    • new Invert section for swapping substituents
  • Color Key (Utilities) — numeric color key labels can be spaced in proportion to their values (previously, spacing was always equal)
  • Effects (Viewing Controls) — global single-layer transparency setting
  • Ensemble Match (Structure Comparison, MD/Ensemble Analysis) — RMSD values can be exported collectively to a text file
  • FindHBond (Structure Analysis, Surface/Binding Analysis) — added option to label H-bonds with distances
  • Fit in Map (Volume Data) — now takes up to 1000 steps (formerly 100)
  • MatchMaker (Structure Comparison) — can be restricted to selected residues
  • Metal Geometry (Structure Analysis) —
    • potential coordination geometries now assessed by "distance RMSD" from idealized atom positions rather than "angle RMSD," as the former is a better indicator of the correct geometry
    • alternate location handling added
    • session support added
    • idealized geometry for cube corrected
  • Minimize Structure (Structure Editing) — allows conjugate gradient minimization (previously just steepest descent)
  • Model Panel (General Controls) —
    • group/ungroup function to collapse multiple entries into a single row; grouping is hierarchical (groups may contain other groups) and multi-model PDBs such as NMR ensembles are grouped by default
    • reorganized to show favorites vs. all instead of mutually exclusive lists of frequently/infrequently used functions
    • save sphgen function to write sphere format for DOCK
  • Multalign Viewer (Sequence) —
    • sequences fetched from UniProt (using the PDB/UniProt Info tool, Fetch by ID, or Multalign Viewer Edit... Add Sequence) include UniProt feature annotations as regions
    • UniProt feature annotations can be mapped as regions onto already open sequences using Info... UniProt Annotations
    • menu changes (Tools renamed Info and some of its entries moved to the File menu)
    • several Region Browser improvements for handling potentially large numbers of annotations, including easier coloring, Info button to report included residue ranges
    • mousing over a region shows the region name in a pop-up "balloon" (can be turned off in the Regions preferences)
    • double-clicking a region opens the Region Browser
    • calculation of region overall RMSD
    • Modeller interface allows including water and/or other HETATM residues from the template in the homology models, some loop refinement
    • system “copy” shortcut (e.g., command-C on Mac) works to copy sequence into text buffer
  • Multiscale Models (Higher-Order Structure) —
    • options to produce packed unit cells
    • multiscale model creation can be limited to specific models by selecting them
  • MD Movie (MD/Ensemble Analysis) —
    • can plot distances and angles vs. frame number, save values to file
    • RMSD map values can be saved to a file
    • trajectory reading speeded up for formats that read their coordinate files directly in the Python layer by adding memory-mapping support (i.e., all formats except PDB, AMBER, xyz, and particle)
    • input option "NAMD (prmtop/DCD)" for those using NAMD with AMBER prmtop files
  • PDB/UniProt Info (Sequence) — fetches UniProt sequence annotations and loads them as regions in Multalign Viewer
  • Surface Color (Volume Data, Surface/Binding Analysis) — added option to report value at mouse position
  • Unit Cell (Higher-Order Structure) — added option to produce packed unit cells
  • ViewDock (Surface/Binding Analysis) — reads Maestro/Glide output
  • Volume Tracer (Volume Data) — which features are shown in the dialog can be saved/restored
New Commands:
  • background — set background color(s) or image
  • changechains — reassign chain IDs
  • fitmap — command implementation of Fit in Map, **plus features not available in that tool**:
    • global search with random initial placement
    • sequential fitting of multiple different structures
    • symmetric fitting of copies of the same structure
  • invert — swap substituents
  • resrenumber — renumber residues
  • ribclass — set ribbon residue class: which atoms control ribbon path and which are hidden by ribbon
  • ribspline — set ribbon path method: B-spline or cardinal spline; control additional smoothing and “stiffness” of cardinal spline ribbon
  • scene — save and restore scenes, which include positions, display status and styles, labels, etc. (see also new tool: Animation)
  • zonesel — select atoms and/or surfaces within a cutoff distance of specified atoms and/or surfaces (this command allows defining zones by surfaces, whereas the standard command-line zone operators < and > refer to atoms only)
Command Changes:
  • addaa — can add to N-terminus (previously just C-terminus)
  • addh
    • less common protonation states of Asp, Glu, Lys, Cys can be specified
    • new default is to consider each model in isolation, otherwise other models in the vicinity may affect hydrogen placement
  • clip — can turn global clipping on and off
  • crystalcontacts — can report residue minimum contact distance, maximum buried SASA
  • findhbond (hbonds) — added option to label H-bonds with distances
  • ksddssp — added -v flag for verbose mode, reports helix and strand residue ranges and whether interstrand relationships are parallel or antiparallel
  • labelopt — significantly enhanced to define a broad range of custom labels for both atoms and residues
  • mask — input volume can be specified as ones (all values 1); previously had to be an existing data set
  • match
    • can move subparts of a model (only certain chains, residues, atoms) instead of the whole model
    • atom specifications can overlap and/or span multiple models
    • options can follow the atom specifications
  • matchmaker — can be restricted to specified residues
  • mcopy — option to copy coordinates relative to target
  • measure
    • area, volume now work on individual surface pieces
    • center to calculate center of mass of map and/or atoms
    • contactArea to report the area of one surface within a cutoff distance of another
    • distance to report the closest distance between one set of atoms and/or surface pieces and another set
    • mapValues to interpolate map values at atom positions, assign as an attribute (command-line implementation of Values at Atom Positions tool)
    • pathLength to report the total length of a set of bonds
    • rotation — the transformation can be reported in the coordinate system of a third model
    • symmetry to identify map symmetry
  • minimize
    • settings for conjugate gradient minimization
    • parts of structures can be ignored
    • syntax simplified, allows freezing atoms without making selections
    • options to suppress caching and re-prepping
  • molmap — symmetry options for making maps corresponding to symmetrical multimers
  • movie — recording size option allows creating movies with image dimensions larger than the Chimera window
  • pauseend option to exit script immediately
  • rmsd — atom specifications can overlap and/or span multiple models
  • scolorzone option (command-line implementation of Color Zone tool)
  • segment — more operations on segmentation regions:
    • directioncolor to color by principal axis orientation
    • exportmask to export the region index mask as a map file
    • sliceimage to create montage images of density map slices
  • set — added singlelayer (global single-layer transparency)
  • shape — added cone
  • sop
    • cap (command implementation of Surface Capping tool)
    • clip to spherically clip volume isosurfaces
    • hideDust (command implementation of Hide Dust tool)
    • zone (command implementation of Surface Zone tool)
  • stereo — implemented ~stereo (equivalent to stereo mono)
  • swapna — new default is to preserve existing glycosidic bond length and angle
  • sym
    • can use the symmetry of another model or of polygons within a cage model from Cage Builder
    • more symmetry groups (tetrahedral, octahedral), products of groups
    • changed syntax for helical and translational symmetries
    • the model number of loaded copies can be specified
    • the resolution of low-res surfaces can be specified
    • can generate BIOMT matrices for the molecule
    • occupancy keyword allows filling only a fraction of positions
  • vop
    • tile to make a single-plane volume from slices of another
    • unroll to make a flat slab from a cylindrical slab
    • zone to mask within or beyond a zone of specified atoms
Notable Bugfixes:
  • Fixed memory leak where closed models were not having their associated memory released. Leak has existed since at least the 1.3 release, but became more widespread in the 1.4 and later releases since presets trigger the condition needed for the leak to occur.
  • The inside ribbon color is now exported (e.g., POV-ray shows it)
  • On Windows, non-western user names now work except for compressed TIFF files and the conic command.
  • Fixed STL export so the triangle normals match the triangles, not one of the vertices.
  • Fixed bond rotation bookkeeping errors that occasionally caused crashes or rotated the wrong atoms.
Known Bugs:
  • surfaces fail for some structures
  • POV-Ray incorrectly renders some of the characters in the fonts Chimera uses, especially the zero
  • Mac OS X problems:
    • in Mac OS X 10.6.4, the display of large surfaces (> 15 million triangles) can cause the machine to freeze requiring a reboot. This is a graphics driver bug affecting both Nvidia and ATI graphics cards.
    • in Mac OS X 10.5, opening and then closing IDLE adds the IDLE menus to the Chimera menus, and trying to use the extra menus generates errors
    • in sequential stereo, the drag selection outline is only visible for a fraction of a second when the mouse button is released
  • Mac OS X with X Windows problems:
    • Observed with 10.5 (Leopard):
      • sometimes display does not update (can be forced by slightly moving the view contents with the mouse)
      • sometimes saved images have a corrupt or "mis-tiled" appearance. Workarounds to try include:
        • showing the Command Line if it is not shown (or if it is shown, hiding it) and then re-saving the image
        • saving the position with command savepos, jiggling the view with the mouse, restoring the position with reset, and then re-saving the image
        • saving a session, then using the native Mac version of Chimera (non-X11) to restore the session and re-save the image
    • Observed with 10.6 (Snow Leopard):
      • Side View may come up blank, but will be filled in when structures are moved
      • closing the Viewing dialog (Side View, Lighting, etc.) causes chimera to crash on next graphics redraw

v1.6 [02-03-12]

General Changes:

  • new Rapid Access interface to frequently used data and tools shown automatically upon startup, but can be hidden/shown at any time by clicking the lightning-bolt icon, or hidden by opening 3D data
  • new fetch type UniProt, protein sequence and annotations
  • default fetch directory set to ~/Downloads/Chimera (previously none) and option to ignore cached data added to Fetch by ID dialog
  • changed default model colors
  • labels drawn in front (default, Background preferences)
  • ribbon cardinal spline option for closer tracking of backbone atom positions, associated parameters for additional smoothing of strand and/or coil, ribbon “stiffness” (molecule model attributes, see also ribspline command)
  • global single-layer transparency, on by default in Effects (previously, single-layer transparency was per-surface and unavailable for ribbons and atoms; this individual surface attribute has been removed). Rendering only the topmost transparent layer simplifies the display and effectively de-emphasizes transparent parts.
  • the background can be set to a vertical multicolor gradient or to an image read from a file
  • Color Actions dialog includes "more..." buttons to show additional background and depth-cueing settings
  • PDB chain "molecule" info reported in Reply Log upon input, shown in status line when the cursor is paused over the chain
  • new residue attribute uniprotIndex (residue number in the corresponding UniProt sequence, determined from PDB header information using a web service provided by the RCSB PDB)
  • symmetry matrices read from mmCIF (previously only PDB)
  • new input/output type, spheres in the sphgen format used by DOCK
  • ViewDock reads Maestro docking output
  • new export type, WebGL (experimental feature)
  • CASTp —
    • pocket information saved in sessions
    • pocket surfaces optionally colored to show hydrophobicity
  • Save Image dialog includes option to save temporary session file
  • maximum image supersampling reduced from 6x6 to 4x4 because high levels increase computational demands without further visible improvement
  • changing the horizontal field of view camera parameter no longer changes the camera Z-position, and changing the width of the graphics window no longer changes either of those
  • saved positions include horizontal field of view value
  • new camera modes: dome, truncated dome
  • BILD/VRML text support added (see BILD .cmov and .font directives)
  • scaling with mouse scroll wheel and touchpad scrolling can be turned off (Mouse preferences)
New Tools:
  • Animation (Utilities) **under development, not fully functional, may change significantly** — save/restore Chimera scenes
  • Cage Builder (Higher-Order Structure) — create polyhedral cages composed of hexagons, pentagons, and other polygons
  • Change Chain IDs (Structure Editing)
  • MultiFit (Volume Data) — simultaneous rigid fitting of multiple structures into density (uses RBVI web server running the program MultiFit from the Sali lab)
  • Palette Editor (Utilities) — create and choose palettes (series of colors and interpolation method; currently used for background color gradients)
  • Renumber Residues (Structure Editing)
Tool Changes:
  • AddCharge (Structure Analysis, Structure Editing) — ATP, ADP, GTP, GDP now treated as standard residues (charge lookup from Amber parameter database, Bryce Group, Manchester)
  • AddH (Structure Editing) —
    • less common protonation states of Asp, Glu, Lys, Cys can be specified
    • new default is to consider each model in isolation, otherwise other models in the vicinity may affect hydrogen placement
  • Adjust Torsions (Structure Editing) — terminal bonds can be rotated
  • Blast Protein (Sequence) — many more columns of information can be shown for pdb hits (ligands, resolution, etc.)
  • Build Structure (Structure Editing) —
    • easier peptide linking with Join Models
    • new Invert section for swapping substituents
  • Color Key (Utilities) — numeric color key labels can be spaced in proportion to their values (previously, spacing was always equal)
  • Effects (Viewing Controls) — global single-layer transparency setting
  • Ensemble Match (Structure Comparison, MD/Ensemble Analysis) — RMSD values can be exported collectively to a text file
  • FindHBond (Structure Analysis, Surface/Binding Analysis) — added option to label H-bonds with distances
  • Fit in Map (Volume Data) — now takes up to 1000 steps (formerly 100)
  • MatchMaker (Structure Comparison) — can be restricted to selected residues
  • Metal Geometry (Structure Analysis) —
    • potential coordination geometries now assessed by "distance RMSD" from idealized atom positions rather than "angle RMSD," as the former is a better indicator of the correct geometry
    • alternate location handling added
    • session support added
    • idealized geometry for cube corrected
  • Minimize Structure (Structure Editing) — allows conjugate gradient minimization (previously just steepest descent)
  • Model Panel (General Controls) —
    • group/ungroup function to collapse multiple entries into a single row; grouping is hierarchical (groups may contain other groups) and multi-model PDBs such as NMR ensembles are grouped by default
    • reorganized to show favorites vs. all instead of mutually exclusive lists of frequently/infrequently used functions
    • save sphgen function to write sphere format for DOCK
  • Multalign Viewer (Sequence) —
    • sequences fetched from UniProt (using the PDB/UniProt Info tool, Fetch by ID, or Multalign Viewer Edit... Add Sequence) include UniProt feature annotations as regions
    • UniProt feature annotations can be mapped as regions onto already open sequences using Info... UniProt Annotations
    • menu changes (Tools renamed Info and some of its entries moved to the File menu)
    • several Region Browser improvements for handling potentially large numbers of annotations, including easier coloring, Info button to report included residue ranges
    • mousing over a region shows the region name in a pop-up "balloon" (can be turned off in the Regions preferences)
    • double-clicking a region opens the Region Browser
    • calculation of region overall RMSD
    • Modeller interface allows including water and/or other HETATM residues from the template in the homology models, some loop refinement
    • system “copy” shortcut (e.g., command-C on Mac) works to copy sequence into text buffer
  • Multiscale Models (Higher-Order Structure) —
    • options to produce packed unit cells
    • multiscale model creation can be limited to specific models by selecting them
  • MD Movie (MD/Ensemble Analysis) —
    • can plot distances and angles vs. frame number, save values to file
    • RMSD map values can be saved to a file
    • trajectory reading speeded up for formats that read their coordinate files directly in the Python layer by adding memory-mapping support (i.e., all formats except PDB, AMBER, xyz, and particle)
    • input option "NAMD (prmtop/DCD)" for those using NAMD with AMBER prmtop files
  • PDB/UniProt Info (Sequence) — fetches UniProt sequence annotations and loads them as regions in Multalign Viewer
  • Surface Color (Volume Data, Surface/Binding Analysis) — added option to report value at mouse position
  • Unit Cell (Higher-Order Structure) — added option to produce packed unit cells
  • ViewDock (Surface/Binding Analysis) — reads Maestro/Glide output
  • Volume Tracer (Volume Data) — which features are shown in the dialog can be saved/restored
New Commands:
  • background — set background color(s) or image
  • changechains — reassign chain IDs
  • fitmap — command implementation of Fit in Map, **plus features not available in that tool**:
    • global search with random initial placement
    • sequential fitting of multiple different structures
    • symmetric fitting of copies of the same structure
  • invert — swap substituents
  • resrenumber — renumber residues
  • ribclass — set ribbon residue class: which atoms control ribbon path and which are hidden by ribbon
  • ribspline — set ribbon path method: B-spline or cardinal spline; control additional smoothing and “stiffness” of cardinal spline ribbon
  • scene — save and restore scenes, which include positions, display status and styles, labels, etc. (see also new tool: Animation)
  • zonesel — select atoms and/or surfaces within a cutoff distance of specified atoms and/or surfaces (this command allows defining zones by surfaces, whereas the standard command-line zone operators < and > refer to atoms only)
Command Changes:
  • addaa — can add to N-terminus (previously just C-terminus)
  • addh
    • less common protonation states of Asp, Glu, Lys, Cys can be specified
    • new default is to consider each model in isolation, otherwise other models in the vicinity may affect hydrogen placement
  • clip — can turn global clipping on and off
  • crystalcontacts — can report residue minimum contact distance, maximum buried SASA
  • findhbond (hbonds) — added option to label H-bonds with distances
  • ksddssp — added -v flag for verbose mode, reports helix and strand residue ranges and whether interstrand relationships are parallel or antiparallel
  • labelopt — significantly enhanced to define a broad range of custom labels for both atoms and residues
  • mask — input volume can be specified as ones (all values 1); previously had to be an existing data set
  • match
    • can move subparts of a model (only certain chains, residues, atoms) instead of the whole model
    • atom specifications can overlap and/or span multiple models
    • options can follow the atom specifications
  • matchmaker — can be restricted to specified residues
  • mcopy — option to copy coordinates relative to target
  • measure
    • area, volume now work on individual surface pieces
    • center to calculate center of mass of map and/or atoms
    • contactArea to report the area of one surface within a cutoff distance of another
    • distance to report the closest distance between one set of atoms and/or surface pieces and another set
    • mapValues to interpolate map values at atom positions, assign as an attribute (command-line implementation of Values at Atom Positions tool)
    • pathLength to report the total length of a set of bonds
    • rotation — the transformation can be reported in the coordinate system of a third model
    • symmetry to identify map symmetry
  • minimize
    • settings for conjugate gradient minimization
    • parts of structures can be ignored
    • syntax simplified, allows freezing atoms without making selections
    • options to suppress caching and re-prepping
  • molmap — symmetry options for making maps corresponding to symmetrical multimers
  • movie — recording size option allows creating movies with image dimensions larger than the Chimera window
  • pauseend option to exit script immediately
  • rmsd — atom specifications can overlap and/or span multiple models
  • scolorzone option (command-line implementation of Color Zone tool)
  • segment — more operations on segmentation regions:
    • directioncolor to color by principal axis orientation
    • exportmask to export the region index mask as a map file
    • sliceimage to create montage images of density map slices
  • set — added singlelayer (global single-layer transparency)
  • shape — added cone
  • sop
    • cap (command implementation of Surface Capping tool)
    • clip to spherically clip volume isosurfaces
    • hideDust (command implementation of Hide Dust tool)
    • zone (command implementation of Surface Zone tool)
  • stereo — implemented ~stereo (equivalent to stereo mono)
  • swapna — new default is to preserve existing glycosidic bond length and angle
  • sym
    • can use the symmetry of another model or of polygons within a cage model from Cage Builder
    • more symmetry groups (tetrahedral, octahedral), products of groups
    • changed syntax for helical and translational symmetries
    • the model number of loaded copies can be specified
    • the resolution of low-res surfaces can be specified
    • can generate BIOMT matrices for the molecule
    • occupancy keyword allows filling only a fraction of positions
  • vop
    • tile to make a single-plane volume from slices of another
    • unroll to make a flat slab from a cylindrical slab
    • zone to mask within or beyond a zone of specified atoms
Notable Bugfixes:
  • Fixed memory leak where closed models were not having their associated memory released. Leak has existed since at least the 1.3 release, but became more widespread in the 1.4 and later releases since presets trigger the condition needed for the leak to occur.
  • The inside ribbon color is now exported (e.g., POV-ray shows it)
  • On Windows, non-western user names now work except for compressed TIFF files and the conic command.
  • Fixed STL export so the triangle normals match the triangles, not one of the vertices.
  • Fixed bond rotation bookkeeping errors that occasionally caused crashes or rotated the wrong atoms.
Known Bugs:
  • surfaces fail for some structures
  • POV-Ray incorrectly renders some of the characters in the fonts Chimera uses, especially the zero
  • Mac OS X problems:
    • in Mac OS X 10.6.4, the display of large surfaces (> 15 million triangles) can cause the machine to freeze requiring a reboot. This is a graphics driver bug affecting both Nvidia and ATI graphics cards.
    • in Mac OS X 10.5, opening and then closing IDLE adds the IDLE menus to the Chimera menus, and trying to use the extra menus generates errors
    • in sequential stereo, the drag selection outline is only visible for a fraction of a second when the mouse button is released
  • Mac OS X with X Windows problems:
    • Observed with 10.5 (Leopard):
      • sometimes display does not update (can be forced by slightly moving the view contents with the mouse)
      • sometimes saved images have a corrupt or "mis-tiled" appearance. Workarounds to try include:
        • showing the Command Line if it is not shown (or if it is shown, hiding it) and then re-saving the image
        • saving the position with command savepos, jiggling the view with the mouse, restoring the position with reset, and then re-saving the image
        • saving a session, then using the native Mac version of Chimera (non-X11) to restore the session and re-save the image
    • Observed with 10.6 (Snow Leopard):
      • Side View may come up blank, but will be filled in when structures are moved
      • closing the Viewing dialog (Side View, Lighting, etc.) causes chimera to crash on next graphics redraw

v1.5.3 [03-20-11]

Contents

  • General Changes
  • New Tools
  • Tool Changes
  • New Commands
  • Command Changes
  • Notable Bugfixes
  • Known Bugs
General Changes:
  • Updated many of the bundled software packages, most notably: Python 2.7, ScientificPython 2.9.0, AmberTools 1.4
  • Actions... Color menu simplified, all options... opens separate dialog with target settings and full set of colors
  • Actions... Atoms/Bonds menu includes controls for ring fill, aromaticity display, nucleotide display
  • start-of-line aliases (defined with alias ^name) now available from top-level Aliases menu
  • selection broadening/narrowing cascades now include "nothing," one level narrower than the original selection
  • new coil selector specifies all non-helix, non-strand amino acid residues
  • default label offsets increased for better readability
  • appearance of small sticks improved
  • subdivision quality default (Effects, interactive presets) raised to 1.5
  • Focus (menu and command) and window command with specified targets now consider window height, not just width
  • for purposes of Focus (menu and command), ribbon display implies display of backbone atoms rather than all atoms of a residue
  • residue label position can be based on primary atom or backbone only rather than all displayed atoms
  • ModBase fetch shows additional model scores, where available
  • PDB fetching improvements — personal PDB directories can be flat or hierarchical, files compressed or not
  • saving to multiple PDB or Mol2 files allows file naming by model name
  • Mol2 files can be written with Amber/GAFF atom types (from Add Charge) instead of Sybyl atom types
  • can read PQR format as produced by PDB2PQR v1.6, assign atomic charge and radius attributes accordingly
  • can read Gromos87 format (single structure, not trajectory)
  • added VRML level-of-detail (LOD) support
  • added General preference, whether to try to place dialogs beside the main window instead of on top (on by default)
  • commands can be copied from the Command History for pasting into another application window
  • most histograms (e.g., Render by Attribute) now automatically adjust their displayed range when a value outside the range is entered
  • Selector Construction Panel removed
  • the --script option (used at startup from the system command-line) now uses quotes to delimit which arguments go to the script, behaves like the runscript command
  • the startup option --script and command runscript run scripts in Chimera's current directory instead of the directory containing the script
New Tools:
  • Metal Geometry (Structure Analysis) — analyze metal coordination geometry
  • Modeller interface - graphical interface to the Modeller homology modeling program (Sali Lab, UCSF)
    • interface currently accessible from the Structure menu in MultAlign Viewer
    • the SaliLab Model Evaluation Server can be called to compute additional model scores
  • Ramachandran Plot (only accessible from Model Panel currently)
  • PDB/UniProt Info (Sequence) — retrieve annotations for PDB entries using a web service from the RCSB (tool is in early stage, may change significantly)
  • Segment Map, Fit to Segments (Volume Data) — these comprise the Segger package (thanks to Greg Pintilie, National Center for Macromolecular Imaging)
  • Small-Angle X-Ray Profile (Higher-Order Structure) — calculate theoretical SAXS profile, compare with experimental profile
Tool Changes:
  • 2D Labels (Utilities) —
    • includes arrows that can be drawn in any orientation
    • 2D labels including text, symbols, and arrows can be written to and read from files (allows transferring labels between sessions, hand-editing, saving labels without saving the entire session, etc.)
  • Add Charge (Structure Analysis, Structure Editing) — added option to show partial charges as labels
  • Axes/Planes (Structure Analysis) — expanded to Axes/Planes/Centroids
  • Blast Protein (Sequence) — query from structure chain includes residues from SEQRES (if present) even if missing from the coordinates
  • Build Structure (Structure Editing) —
    • new Join Models section bonds and merges two models, moving one of them to form the appropriate bond (previously required laborious hand-positioning)
    • other sections renamed to better reflect their uses: Start Structure, Modify Structure, Adjust Bonds
    • each section now uses an Apply button
  • Color Editor (Utilities) — if a color component value > 1 and ≤ 255 is entered, it is automatically divided by 255 to convert it to the 0–1 range
  • Coulombic Surface Coloring (Surface/Binding Analysis) — can generate a grid of the values (a volume dataset), thus allowing coloring surface caps, showing isosurfaces, saving to a file, etc.
  • Distances, Angles/Torsions (Structure Analysis) —
    • added option to select the corresponding atoms/bonds when a measurement is chosen in the table
    • angle monitors saved in sessions
  • Fit in Map (Volume Data) — correlation can be calculated about zero (now default) or mean values
  • Find Clashes/Contacts (Structure Analysis, Surface/Binding Analysis) — allows checking for interactions between two independently designated sets of atoms (not just a designated set against itself or all other atoms)
  • FindHBond (Structure Analysis, Surface/Binding Analysis) —
    • allows finding only those H-bonds between the selection and an independently designated set of atoms
    • pseudobonds drawn to hydrogens if present instead of donor heavy atoms
  • Lighting (Viewing Controls) —
    • new modes with different numbers/types of lights, including ambient-only
    • interface reorganized and simplified, advanced section removed (new lighting command provides access to those settings)
  • Match → Align (Structure Comparison, Sequence) — in addition to the RMSD and number of equivalenced positions (alignment length), reports Structural Distance Measure (SDM) and Q-score values
  • MD Movie (MD/Ensemble Analysis) —
    • support added for "particle" trajectory format, designed for coarse-grained systems
    • can read trajectory from multiple XYZ files, one per frame
    • can read/concatenate multiple DCD trajectory files
    • reads atomic charges from some topology formats (PSF, Amber prmtop)
    • can perform clustering (same method as Ensemble Cluster tool)
    • better integrated with coordset command
    • controller dialog will restore from a saved session if the entire trajectory was read in before saving
  • Measure and Color Blobs (Surface/Binding Analysis, Volume Data) —
    • can generate a new color for each blob
    • can draw bounding box aligned with principal axes of inertia
  • Minimize Structure (Structure Editing) — can remember settings of secondary dialogs (Dock Prep etc.) for optional use in subsequent minimizations
  • Model Panel (General Controls) — added biological unit and Ramachandran plot functions
  • Movie Recorder (Utilities) — variable bit rate encoding (Q=8) now default
  • Multalign Viewer (Sequence) —
    • Blast protein search available from Tools menu
    • trees saved in sessions
    • single-sequence files can be read/written
    • can read alignments (only) from HSSP files
    • vertical scrolling with mouse scroll wheel
    • can add sequence(s) from a file (previously just from structure or pasted as plain test)
    • alignment headers may contain symbols (circle, square, diamond, star)
  • Phantom Force Feedback (Volume Data) — removed
  • Render by Attribute (Depiction, Structure Analysis) — for convenience in setting colors, added built-in palettes and the ability to reverse color order with a single click
  • ResProp (Structure Analysis) — coloring section removed
  • Rotamers (Structure Editing) — the existing sidechains can be retained
  • Surfnet (Surface/Binding Analysis) — simplified into a single dialog without loss of functionality
  • Thermal Ellipsoids (Structure Analysis) —
    • anisotropic B-factors read from CIF/mmCIF (previously only PDB)
    • depictions saved in sessions
    • possible depictions include ellipsoid principal axes and/or principal ellipses in addition to the ellipsoids themselves
    • includes Presets menu for rapid access to predefined combinations of options
  • Transform Coordinates (Movement) — renamed from Transform Molecule Coordinates, now works on all model types
  • Volume Filter (Volume Data) —
    • Gaussian filtering more memory-efficient, allows specifying output value type
    • added Flatten filter
New Commands:
  • coulombic — command-line implementation of Coulombic Surface Coloring
  • lighting — adjust lighting and shininess
Command Changes:
  • 2dlabels
    • includes 2D arrows in any orientation
    • 2D labels including text, symbols, and arrows can be written to and read from files (allows transferring labels between sessions, hand-editing, saving labels without saving the entire session, etc.)
  • align — can align an axis or plane object (previously worked only on atoms)
  • angle — can measure angles between axes and/or planes
  • aniso — added options for display of thermal ellipsoid principal axes and/or principal ellipses, other changes as listed above for Thermal Ellipsoids
  • close — more than one model number can be given
  • define — can calculate centroids (previously just axes and planes)
  • distance — can measure distances involving axes, planes, and/or centroids
  • findclash — allows checking for interactions between two independently specified sets of atoms (not just a specified set against itself or all other atoms)
  • findhbond (hbonds) — allows finding only those H-bonds between the selection and an independently designated set of atoms; pseudobonds drawn to hydrogens if present instead of donor heavy atoms
  • help — use without arguments opens the search dialog
  • measure — added spine calculation of a path along the center line of a segmentation region from Segment Map
  • morph — added nogui true option to suppress MD Movie dialog
  • movie
    • variable bit rate encoding (Q=8) now default
    • new crossfade option for transition by linear interpolation
  • nucleotides — added ~nucleotides for convenience (equivalent to nuc side atoms)
  • rock, roll, turn — a center of rotation method can be specified just for executing the command (for example, allows rotating around the center of view with the command even if a different center is used for rotation with the mouse)
  • setattr — added M flag, all applicable models
  • shape — can generate ellipsoids, rectangles, flat ribbons, apply specified rotations to some shapes
  • swapaa — the existing sidechains can be retained
  • sym — option to generate low-res surfaces instead of atomic copies for efficiency on large systems
  • vop — added flatten and unbend operations, gaussian allows specifying output value type
  • redundant commands removed: load, source, rescolor, resrepr, x3dsave, brotation, push, pop
Notable Bugfixes:
  • transparent ribbons no longer contain extraneous disks
  • eliminated blocky artifacts that could occur around labels in a scene with transparency
  • when possible, shadows are smoother
  • shadows and labels can be used at the same time
  • saving images now uses OpenGL framebuffer objects for off-screen rendering to work around problems with some platforms (mostly older Macs and some Linux systems)
Known Bugs:
  • surfaces fail for some structures
  • POV-Ray incorrectly renders some of the characters in the fonts Chimera uses, especially the zero
  • the inside ribbon color is not exported (e.g., POV-ray does not show it)
  • Gromacs trajectories from version 4.5.1 (and later) do not work. Version 4.0.2 (and earlier) trajectories do work. The status of intermediate trajectory versions is unknown at this time.
  • Mac OS X problems:
    • in Mac OS X 10.6.4, the display of large surfaces (> 15 million triangles) can cause the machine to freeze requiring a reboot. This is a graphics driver bug effecting both Nvidia and ATI graphics cards.
    • in Mac OS X 10.5, opening and then closing IDLE adds the IDLE menus to the Chimera menus, and trying to use the extra menus generates errors
    • in sequential stereo, the drag selection outline is only visible for a fraction of a second when the mouse button is released
  • Mac OS X with X Windows problems:
    • Observed with 10.5 (Leopard):
      • sometimes display does not update (can be forced by slightly moving the view contents with the mouse)
      • sometimes saved images have a corrupt or "mis-tiled" appearance. Workarounds to try include:
        • showing the Command Line if it is not shown (or if it is shown, hiding it) and then re-saving the image
        • saving the position with command savepos, jiggling the view with the mouse, restoring the position with reset, and then re-saving the image
        • saving a session, then using the native Mac version of Chimera (non-X11) to restore the session and re-save the image
    • Observed with 10.6 (Snow Leopard):
      • Side View may come up blank, but will be filled in when structures are moved
      • closing the Viewing dialog (Side View, Lighting, etc.) causes chimera to crash on next graphics redraw

v1.5.2 [01-30-11]

Contents

  • General Changes
  • New Tools
  • Tool Changes
  • New Commands
  • Command Changes
  • Notable Bugfixes
  • Known Bugs
General Changes:
  • Updated many of the bundled software packages, most notably: Python 2.7, ScientificPython 2.9.0, AmberTools 1.4
  • Actions... Color menu simplified, all options... opens separate dialog with target settings and full set of colors
  • Actions... Atoms/Bonds menu includes controls for ring fill, aromaticity display, nucleotide display
  • start-of-line aliases (defined with alias ^name) now available from top-level Aliases menu
  • selection broadening/narrowing cascades now include "nothing," one level narrower than the original selection
  • new coil selector specifies all non-helix, non-strand amino acid residues
  • default label offsets increased for better readability
  • appearance of small sticks improved
  • subdivision quality default (Effects, interactive presets) raised to 1.5
  • Focus (menu and command) and window command with specified targets now consider window height, not just width
  • for purposes of Focus (menu and command), ribbon display implies display of backbone atoms rather than all atoms of a residue
  • residue label position can be based on primary atom or backbone only rather than all displayed atoms
  • ModBase fetch shows additional model scores, where available
  • PDB fetching improvements — personal PDB directories can be flat or hierarchical, files compressed or not
  • saving to multiple PDB or Mol2 files allows file naming by model name
  • Mol2 files can be written with Amber/GAFF atom types (from Add Charge) instead of Sybyl atom types
  • can read PQR format as produced by PDB2PQR v1.6, assign atomic charge and radius attributes accordingly
  • can read Gromos87 format (single structure, not trajectory)
  • added VRML level-of-detail (LOD) support
  • added General preference, whether to try to place dialogs beside the main window instead of on top (on by default)
  • commands can be copied from the Command History for pasting into another application window
  • most histograms (e.g., Render by Attribute) now automatically adjust their displayed range when a value outside the range is entered
  • Selector Construction Panel removed
  • the --script option (used at startup from the system command-line) now uses quotes to delimit which arguments go to the script, behaves like the runscript command
  • the startup option --script and command runscript run scripts in Chimera's current directory instead of the directory containing the script
New Tools:
  • Metal Geometry (Structure Analysis) — analyze metal coordination geometry
  • Modeller interface - graphical interface to the Modeller homology modeling program (Sali Lab, UCSF)
    • interface currently accessible from the Structure menu in MultAlign Viewer
    • the SaliLab Model Evaluation Server can be called to compute additional model scores
  • Ramachandran Plot (only accessible from Model Panel currently)
  • PDB/UniProt Info (Sequence) — retrieve annotations for PDB entries using a web service from the RCSB (tool is in early stage, may change significantly)
  • Segment Map, Fit to Segments (Volume Data) — these comprise the Segger package (thanks to Greg Pintilie, National Center for Macromolecular Imaging)
  • Small-Angle X-Ray Profile (Higher-Order Structure) — calculate theoretical SAXS profile, compare with experimental profile
Tool Changes:
  • 2D Labels (Utilities) —
    • includes arrows that can be drawn in any orientation
    • 2D labels including text, symbols, and arrows can be written to and read from files (allows transferring labels between sessions, hand-editing, saving labels without saving the entire session, etc.)
  • Add Charge (Structure Analysis, Structure Editing) — added option to show partial charges as labels
  • Axes/Planes (Structure Analysis) — expanded to Axes/Planes/Centroids
  • Blast Protein (Sequence) — query from structure chain includes residues from SEQRES (if present) even if missing from the coordinates
  • Build Structure (Structure Editing) —
    • new Join Models section bonds and merges two models, moving one of them to form the appropriate bond (previously required laborious hand-positioning)
    • other sections renamed to better reflect their uses: Start Structure, Modify Structure, Adjust Bonds
    • each section now uses an Apply button
  • Color Editor (Utilities) — if a color component value > 1 and ≤ 255 is entered, it is automatically divided by 255 to convert it to the 0–1 range
  • Coulombic Surface Coloring (Surface/Binding Analysis) — can generate a grid of the values (a volume dataset), thus allowing coloring surface caps, showing isosurfaces, saving to a file, etc.
  • Distances, Angles/Torsions (Structure Analysis) —
    • added option to select the corresponding atoms/bonds when a measurement is chosen in the table
    • angle monitors saved in sessions
  • Fit in Map (Volume Data) — correlation can be calculated about zero (now default) or mean values
  • Find Clashes/Contacts (Structure Analysis, Surface/Binding Analysis) — allows checking for interactions between two independently designated sets of atoms (not just a designated set against itself or all other atoms)
  • FindHBond (Structure Analysis, Surface/Binding Analysis) —
    • allows finding only those H-bonds between the selection and an independently designated set of atoms
    • pseudobonds drawn to hydrogens if present instead of donor heavy atoms
  • Lighting (Viewing Controls) —
    • new modes with different numbers/types of lights, including ambient-only
    • interface reorganized and simplified, advanced section removed (new lighting command provides access to those settings)
  • Match → Align (Structure Comparison, Sequence) — in addition to the RMSD and number of equivalenced positions (alignment length), reports Structural Distance Measure (SDM) and Q-score values
  • MD Movie (MD/Ensemble Analysis) —
    • support added for "particle" trajectory format, designed for coarse-grained systems
    • can read trajectory from multiple XYZ files, one per frame
    • can read/concatenate multiple DCD trajectory files
    • reads atomic charges from some topology formats (PSF, Amber prmtop)
    • can perform clustering (same method as Ensemble Cluster tool)
    • better integrated with coordset command
    • controller dialog will restore from a saved session if the entire trajectory was read in before saving
  • Measure and Color Blobs (Surface/Binding Analysis, Volume Data) —
    • can generate a new color for each blob
    • can draw bounding box aligned with principal axes of inertia
  • Minimize Structure (Structure Editing) — can remember settings of secondary dialogs (Dock Prep etc.) for optional use in subsequent minimizations
  • Model Panel (General Controls) — added biological unit and Ramachandran plot functions
  • Movie Recorder (Utilities) — variable bit rate encoding (Q=8) now default
  • Multalign Viewer (Sequence) —
    • Blast protein search available from Tools menu
    • trees saved in sessions
    • single-sequence files can be read/written
    • can read alignments (only) from HSSP files
    • vertical scrolling with mouse scroll wheel
    • can add sequence(s) from a file (previously just from structure or pasted as plain test)
    • alignment headers may contain symbols (circle, square, diamond, star)
  • Phantom Force Feedback (Volume Data) — removed
  • Render by Attribute (Depiction, Structure Analysis) — for convenience in setting colors, added built-in palettes and the ability to reverse color order with a single click
  • ResProp (Structure Analysis) — coloring section removed
  • Rotamers (Structure Editing) — the existing sidechains can be retained
  • Surfnet (Surface/Binding Analysis) — simplified into a single dialog without loss of functionality
  • Thermal Ellipsoids (Structure Analysis) —
    • anisotropic B-factors read from CIF/mmCIF (previously only PDB)
    • depictions saved in sessions
    • possible depictions include ellipsoid principal axes and/or principal ellipses in addition to the ellipsoids themselves
    • includes Presets menu for rapid access to predefined combinations of options
  • Transform Coordinates (Movement) — renamed from Transform Molecule Coordinates, now works on all model types
  • Volume Filter (Volume Data) —
    • Gaussian filtering more memory-efficient, allows specifying output value type
    • added Flatten filter
New Commands:
  • coulombic — command-line implementation of Coulombic Surface Coloring
  • lighting — adjust lighting and shininess
Command Changes:
  • 2dlabels
    • includes 2D arrows in any orientation
    • 2D labels including text, symbols, and arrows can be written to and read from files (allows transferring labels between sessions, hand-editing, saving labels without saving the entire session, etc.)
  • align — can align an axis or plane object (previously worked only on atoms)
  • angle — can measure angles between axes and/or planes
  • aniso — added options for display of thermal ellipsoid principal axes and/or principal ellipses, other changes as listed above for Thermal Ellipsoids
  • close — more than one model number can be given
  • define — can calculate centroids (previously just axes and planes)
  • distance — can measure distances involving axes, planes, and/or centroids
  • findclash — allows checking for interactions between two independently specified sets of atoms (not just a specified set against itself or all other atoms)
  • findhbond (hbonds) — allows finding only those H-bonds between the selection and an independently designated set of atoms; pseudobonds drawn to hydrogens if present instead of donor heavy atoms
  • help — use without arguments opens the search dialog
  • measure — added spine calculation of a path along the center line of a segmentation region from Segment Map
  • morph — added nogui true option to suppress MD Movie dialog
  • movie
    • variable bit rate encoding (Q=8) now default
    • new crossfade option for transition by linear interpolation
  • nucleotides — added ~nucleotides for convenience (equivalent to nuc side atoms)
  • rock, roll, turn — a center of rotation method can be specified just for executing the command (for example, allows rotating around the center of view with the command even if a different center is used for rotation with the mouse)
  • setattr — added M flag, all applicable models
  • shape — can generate ellipsoids, rectangles, flat ribbons, apply specified rotations to some shapes
  • swapaa — the existing sidechains can be retained
  • sym — option to generate low-res surfaces instead of atomic copies for efficiency on large systems
  • vop — added flatten and unbend operations, gaussian allows specifying output value type
  • redundant commands removed: load, source, rescolor, resrepr, x3dsave, brotation, push, pop
Notable Bugfixes:
  • transparent ribbons no longer contain extraneous disks
  • eliminated blocky artifacts that could occur around labels in a scene with transparency
  • when possible, shadows are smoother
  • shadows and labels can be used at the same time
  • saving images now uses OpenGL framebuffer objects for off-screen rendering to work around problems with some platforms (mostly older Macs and some Linux systems)
Known Bugs:
  • surfaces fail for some structures
  • POV-Ray incorrectly renders some of the characters in the fonts Chimera uses, especially the zero
  • the inside ribbon color is not exported (e.g., POV-ray does not show it)
  • Gromacs trajectories from version 4.5.1 (and later) do not work. Version 4.0.2 (and earlier) trajectories do work. The status of intermediate trajectory versions is unknown at this time.
  • Mac OS X problems:
    • in Mac OS X 10.6.4, the display of large surfaces (> 15 million triangles) can cause the machine to freeze requiring a reboot. This is a graphics driver bug effecting both Nvidia and ATI graphics cards.
    • in Mac OS X 10.5, opening and then closing IDLE adds the IDLE menus to the Chimera menus, and trying to use the extra menus generates errors
    • in sequential stereo, the drag selection outline is only visible for a fraction of a second when the mouse button is released
  • Mac OS X with X Windows problems:
    • Observed with 10.5 (Leopard):
      • sometimes display does not update (can be forced by slightly moving the view contents with the mouse)
      • sometimes saved images have a corrupt or "mis-tiled" appearance. Workarounds to try include:
        • showing the Command Line if it is not shown (or if it is shown, hiding it) and then re-saving the image
        • saving the position with command savepos, jiggling the view with the mouse, restoring the position with reset, and then re-saving the image
        • saving a session, then using the native Mac version of Chimera (non-X11) to restore the session and re-save the image
    • Observed with 10.6 (Snow Leopard):
      • Side View may come up blank, but will be filled in when structures are moved
      • closing the Viewing dialog (Side View, Lighting, etc.) causes chimera to crash on next graphics redraw

v1.5.1 [01-15-11]

Contents

  • General Changes
  • New Tools
  • Tool Changes
  • New Commands
  • Command Changes
  • Notable Bugfixes
  • Known Bugs
General Changes:
  • Updated many of the bundled software packages, most notably: Python 2.7, ScientificPython 2.9.0, AmberTools 1.4
  • Actions... Color menu simplified, all options... opens separate dialog with target settings and full set of colors
  • Actions... Atoms/Bonds menu includes controls for ring fill, aromaticity display, nucleotide display
  • start-of-line aliases (defined with alias ^name) now available from top-level Aliases menu
  • selection broadening/narrowing cascades now include "nothing," one level narrower than the original selection
  • new coil selector specifies all non-helix, non-strand amino acid residues
  • default label offsets increased for better readability
  • appearance of small sticks improved
  • subdivision quality default (Effects, interactive presets) raised to 1.5
  • Focus (menu and command) and window command with specified targets now consider window height, not just width
  • for purposes of Focus (menu and command), ribbon display implies display of backbone atoms rather than all atoms of a residue
  • residue label position can be based on primary atom or backbone only rather than all displayed atoms
  • ModBase fetch shows additional model scores, where available
  • PDB fetching improvements — personal PDB directories can be flat or hierarchical, files compressed or not
  • saving to multiple PDB or Mol2 files allows file naming by model name
  • Mol2 files can be written with Amber/GAFF atom types (from Add Charge) instead of Sybyl atom types
  • can read PQR format as produced by PDB2PQR v1.6, assign atomic charge and radius attributes accordingly
  • can read Gromos87 format (single structure, not trajectory)
  • added VRML level-of-detail (LOD) support
  • added General preference, whether to try to place dialogs beside the main window instead of on top (on by default)
  • commands can be copied from the Command History for pasting into another application window
  • most histograms (e.g., Render by Attribute) now automatically adjust their displayed range when a value outside the range is entered
  • Selector Construction Panel removed
  • the --script option (used at startup from the system command-line) now uses quotes to delimit which arguments go to the script, behaves like the runscript command
  • the startup option --script and command runscript run scripts in Chimera's current directory instead of the directory containing the script
New Tools:
  • Metal Geometry (Structure Analysis) — analyze metal coordination geometry
  • Modeller interface - graphical interface to the Modeller homology modeling program (Sali Lab, UCSF)
    • interface currently accessible from the Structure menu in MultAlign Viewer
    • the SaliLab Model Evaluation Server can be called to compute additional model scores
  • Ramachandran Plot (only accessible from Model Panel currently)
  • PDB/UniProt Info (Sequence) — retrieve annotations for PDB entries using a web service from the RCSB (tool is in early stage, may change significantly)
  • Segment Map, Fit to Segments (Volume Data) — these comprise the Segger package (thanks to Greg Pintilie, National Center for Macromolecular Imaging)
  • Small-Angle X-Ray Profile (Higher-Order Structure) — calculate theoretical SAXS profile, compare with experimental profile
Tool Changes:
  • 2D Labels (Utilities) —
    • includes arrows that can be drawn in any orientation
    • 2D labels including text, symbols, and arrows can be written to and read from files (allows transferring labels between sessions, hand-editing, saving labels without saving the entire session, etc.)
  • Add Charge (Structure Analysis, Structure Editing) — added option to show partial charges as labels
  • Axes/Planes (Structure Analysis) — expanded to Axes/Planes/Centroids
  • Blast Protein (Sequence) — query from structure chain includes residues from SEQRES (if present) even if missing from the coordinates
  • Build Structure (Structure Editing) —
    • new Join Models section bonds and merges two models, moving one of them to form the appropriate bond (previously required laborious hand-positioning)
    • other sections renamed to better reflect their uses: Start Structure, Modify Structure, Adjust Bonds
    • each section now uses an Apply button
  • Color Editor (Utilities) — if a color component value > 1 and ≤ 255 is entered, it is automatically divided by 255 to convert it to the 0–1 range
  • Coulombic Surface Coloring (Surface/Binding Analysis) — can generate a grid of the values (a volume dataset), thus allowing coloring surface caps, showing isosurfaces, saving to a file, etc.
  • Distances, Angles/Torsions (Structure Analysis) —
    • added option to select the corresponding atoms/bonds when a measurement is chosen in the table
    • angle monitors saved in sessions
  • Fit in Map (Volume Data) — correlation can be calculated about zero (now default) or mean values
  • Find Clashes/Contacts (Structure Analysis, Surface/Binding Analysis) — allows checking for interactions between two independently designated sets of atoms (not just a designated set against itself or all other atoms)
  • FindHBond (Structure Analysis, Surface/Binding Analysis) —
    • allows finding only those H-bonds between the selection and an independently designated set of atoms
    • pseudobonds drawn to hydrogens if present instead of donor heavy atoms
  • Lighting (Viewing Controls) —
    • new modes with different numbers/types of lights, including ambient-only
    • interface reorganized and simplified, advanced section removed (new lighting command provides access to those settings)
  • Match → Align (Structure Comparison, Sequence) — in addition to the RMSD and number of equivalenced positions (alignment length), reports Structural Distance Measure (SDM) and Q-score values
  • MD Movie (MD/Ensemble Analysis) —
    • support added for "particle" trajectory format, designed for coarse-grained systems
    • can read trajectory from multiple XYZ files, one per frame
    • can read/concatenate multiple DCD trajectory files
    • reads atomic charges from some topology formats (PSF, Amber prmtop)
    • can perform clustering (same method as Ensemble Cluster tool)
    • better integrated with coordset command
    • controller dialog will restore from a saved session if the entire trajectory was read in before saving
  • Measure and Color Blobs (Surface/Binding Analysis, Volume Data) —
    • can generate a new color for each blob
    • can draw bounding box aligned with principal axes of inertia
  • Minimize Structure (Structure Editing) — can remember settings of secondary dialogs (Dock Prep etc.) for optional use in subsequent minimizations
  • Model Panel (General Controls) — added biological unit and Ramachandran plot functions
  • Movie Recorder (Utilities) — variable bit rate encoding (Q=8) now default
  • Multalign Viewer (Sequence) —
    • Blast protein search available from Tools menu
    • trees saved in sessions
    • single-sequence files can be read/written
    • can read alignments (only) from HSSP files
    • vertical scrolling with mouse scroll wheel
    • can add sequence(s) from a file (previously just from structure or pasted as plain test)
    • alignment headers may contain symbols (circle, square, diamond, star)
  • Phantom Force Feedback (Volume Data) — removed
  • Render by Attribute (Depiction, Structure Analysis) — for convenience in setting colors, added built-in palettes and the ability to reverse color order with a single click
  • ResProp (Structure Analysis) — coloring section removed
  • Rotamers (Structure Editing) — the existing sidechains can be retained
  • Surfnet (Surface/Binding Analysis) — simplified into a single dialog without loss of functionality
  • Thermal Ellipsoids (Structure Analysis) —
    • anisotropic B-factors read from CIF/mmCIF (previously only PDB)
    • depictions saved in sessions
    • possible depictions include ellipsoid principal axes and/or principal ellipses in addition to the ellipsoids themselves
    • includes Presets menu for rapid access to predefined combinations of options
  • Transform Coordinates (Movement) — renamed from Transform Molecule Coordinates, now works on all model types
  • Volume Filter (Volume Data) —
    • Gaussian filtering more memory-efficient, allows specifying output value type
    • added Flatten filter
New Commands:
  • coulombic — command-line implementation of Coulombic Surface Coloring
  • lighting — adjust lighting and shininess
Command Changes:
  • 2dlabels
    • includes 2D arrows in any orientation
    • 2D labels including text, symbols, and arrows can be written to and read from files (allows transferring labels between sessions, hand-editing, saving labels without saving the entire session, etc.)
  • align — can align an axis or plane object (previously worked only on atoms)
  • angle — can measure angles between axes and/or planes
  • aniso — added options for display of thermal ellipsoid principal axes and/or principal ellipses, other changes as listed above for Thermal Ellipsoids
  • close — more than one model number can be given
  • define — can calculate centroids (previously just axes and planes)
  • distance — can measure distances involving axes, planes, and/or centroids
  • findclash — allows checking for interactions between two independently specified sets of atoms (not just a specified set against itself or all other atoms)
  • findhbond (hbonds) — allows finding only those H-bonds between the selection and an independently designated set of atoms; pseudobonds drawn to hydrogens if present instead of donor heavy atoms
  • help — use without arguments opens the search dialog
  • measure — added spine calculation of a path along the center line of a segmentation region from Segment Map
  • morph — added nogui true option to suppress MD Movie dialog
  • movie
    • variable bit rate encoding (Q=8) now default
    • new crossfade option for transition by linear interpolation
  • nucleotides — added ~nucleotides for convenience (equivalent to nuc side atoms)
  • rock, roll, turn — a center of rotation method can be specified just for executing the command (for example, allows rotating around the center of view with the command even if a different center is used for rotation with the mouse)
  • setattr — added M flag, all applicable models
  • shape — can generate ellipsoids, rectangles, flat ribbons, apply specified rotations to some shapes
  • swapaa — the existing sidechains can be retained
  • sym — option to generate low-res surfaces instead of atomic copies for efficiency on large systems
  • vop — added flatten and unbend operations, gaussian allows specifying output value type
  • redundant commands removed: load, source, rescolor, resrepr, x3dsave, brotation, push, pop
Notable Bugfixes:
  • transparent ribbons no longer contain extraneous disks
  • eliminated blocky artifacts that could occur around labels in a scene with transparency
  • when possible, shadows are smoother
  • shadows and labels can be used at the same time
  • saving images now uses OpenGL framebuffer objects for off-screen rendering to work around problems with some platforms (mostly older Macs and some Linux systems)
Known Bugs:
  • surfaces fail for some structures
  • POV-Ray incorrectly renders some of the characters in the fonts Chimera uses, especially the zero
  • the inside ribbon color is not exported (e.g., POV-ray does not show it)
  • Gromacs trajectories from version 4.5.1 (and later) do not work. Version 4.0.2 (and earlier) trajectories do work. The status of intermediate trajectory versions is unknown at this time.
  • Mac OS X problems:
    • in Mac OS X 10.6.4, the display of large surfaces (> 15 million triangles) can cause the machine to freeze requiring a reboot. This is a graphics driver bug effecting both Nvidia and ATI graphics cards.
    • in Mac OS X 10.5, opening and then closing IDLE adds the IDLE menus to the Chimera menus, and trying to use the extra menus generates errors
    • in sequential stereo, the drag selection outline is only visible for a fraction of a second when the mouse button is released
  • Mac OS X with X Windows problems:
    • Observed with 10.5 (Leopard):
      • sometimes display does not update (can be forced by slightly moving the view contents with the mouse)
      • sometimes saved images have a corrupt or "mis-tiled" appearance. Workarounds to try include:
        • showing the Command Line if it is not shown (or if it is shown, hiding it) and then re-saving the image
        • saving the position with command savepos, jiggling the view with the mouse, restoring the position with reset, and then re-saving the image
        • saving a session, then using the native Mac version of Chimera (non-X11) to restore the session and re-save the image
    • Observed with 10.6 (Snow Leopard):
      • Side View may come up blank, but will be filled in when structures are moved
      • closing the Viewing dialog (Side View, Lighting, etc.) causes chimera to crash on next graphics redraw

v1.5 [10-24-10]

Contents

  • General Changes
  • New Tools
  • Tool Changes
  • New Commands
  • Command Changes
  • Notable Bugfixes
  • Known Bugs
General Changes:
  • Updated many of the bundled software packages, most notably: Python 2.7, ScientificPython 2.9.0, AmberTools 1.4
  • Actions... Color menu simplified, all options... opens separate dialog with target settings and full set of colors
  • Actions... Atoms/Bonds menu includes controls for ring fill, aromaticity display, nucleotide display
  • start-of-line aliases (defined with alias ^name) now available from top-level Aliases menu
  • selection broadening/narrowing cascades now include "nothing," one level narrower than the original selection
  • new coil selector specifies all non-helix, non-strand amino acid residues
  • default label offsets increased for better readability
  • appearance of small sticks improved
  • subdivision quality default (Effects, interactive presets) raised to 1.5
  • Focus (menu and command) and window command with specified targets now consider window height, not just width
  • for purposes of Focus (menu and command), ribbon display implies display of backbone atoms rather than all atoms of a residue
  • residue label position can be based on primary atom or backbone only rather than all displayed atoms
  • ModBase fetch shows additional model scores, where available
  • PDB fetching improvements — personal PDB directories can be flat or hierarchical, files compressed or not
  • saving to multiple PDB or Mol2 files allows file naming by model name
  • Mol2 files can be written with Amber/GAFF atom types (from Add Charge) instead of Sybyl atom types
  • can read PQR format as produced by PDB2PQR v1.6, assign atomic charge and radius attributes accordingly
  • can read Gromos87 format (single structure, not trajectory)
  • added VRML level-of-detail (LOD) support
  • added General preference, whether to try to place dialogs beside the main window instead of on top (on by default)
  • commands can be copied from the Command History for pasting into another application window
  • most histograms (e.g., Render by Attribute) now automatically adjust their displayed range when a value outside the range is entered
  • Selector Construction Panel removed
  • the --script option (used at startup from the system command-line) now uses quotes to delimit which arguments go to the script, behaves like the runscript command
  • the startup option --script and command runscript run scripts in Chimera's current directory instead of the directory containing the script
New Tools:
  • Metal Geometry (Structure Analysis) — analyze metal coordination geometry
  • Modeller interface - graphical interface to the Modeller homology modeling program (Sali Lab, UCSF)
    • interface currently accessible from the Structure menu in MultAlign Viewer
    • the SaliLab Model Evaluation Server can be called to compute additional model scores
  • Ramachandran Plot (only accessible from Model Panel currently)
  • PDB/UniProt Info (Sequence) — retrieve annotations for PDB entries using a web service from the RCSB (tool is in early stage, may change significantly)
  • Segment Map, Fit to Segments (Volume Data) — these comprise the Segger package (thanks to Greg Pintilie, National Center for Macromolecular Imaging)
  • Small-Angle X-Ray Profile (Higher-Order Structure) — calculate theoretical SAXS profile, compare with experimental profile
Tool Changes:
  • 2D Labels (Utilities) —
    • includes arrows that can be drawn in any orientation
    • 2D labels including text, symbols, and arrows can be written to and read from files (allows transferring labels between sessions, hand-editing, saving labels without saving the entire session, etc.)
  • Add Charge (Structure Analysis, Structure Editing) — added option to show partial charges as labels
  • Axes/Planes (Structure Analysis) — expanded to Axes/Planes/Centroids
  • Blast Protein (Sequence) — query from structure chain includes residues from SEQRES (if present) even if missing from the coordinates
  • Build Structure (Structure Editing) —
    • new Join Models section bonds and merges two models, moving one of them to form the appropriate bond (previously required laborious hand-positioning)
    • other sections renamed to better reflect their uses: Start Structure, Modify Structure, Adjust Bonds
    • each section now uses an Apply button
  • Color Editor (Utilities) — if a color component value > 1 and ≤ 255 is entered, it is automatically divided by 255 to convert it to the 0–1 range
  • Coulombic Surface Coloring (Surface/Binding Analysis) — can generate a grid of the values (a volume dataset), thus allowing coloring surface caps, showing isosurfaces, saving to a file, etc.
  • Distances, Angles/Torsions (Structure Analysis) —
    • added option to select the corresponding atoms/bonds when a measurement is chosen in the table
    • angle monitors saved in sessions
  • Fit in Map (Volume Data) — correlation can be calculated about zero (now default) or mean values
  • Find Clashes/Contacts (Structure Analysis, Surface/Binding Analysis) — allows checking for interactions between two independently designated sets of atoms (not just a designated set against itself or all other atoms)
  • FindHBond (Structure Analysis, Surface/Binding Analysis) —
    • allows finding only those H-bonds between the selection and an independently designated set of atoms
    • pseudobonds drawn to hydrogens if present instead of donor heavy atoms
  • Lighting (Viewing Controls) —
    • new modes with different numbers/types of lights, including ambient-only
    • interface reorganized and simplified, advanced section removed (new lighting command provides access to those settings)
  • Match → Align (Structure Comparison, Sequence) — in addition to the RMSD and number of equivalenced positions (alignment length), reports Structural Distance Measure (SDM) and Q-score values
  • MD Movie (MD/Ensemble Analysis) —
    • support added for "particle" trajectory format, designed for coarse-grained systems
    • can read trajectory from multiple XYZ files, one per frame
    • can read/concatenate multiple DCD trajectory files
    • reads atomic charges from some topology formats (PSF, Amber prmtop)
    • can perform clustering (same method as Ensemble Cluster tool)
    • better integrated with coordset command
    • controller dialog will restore from a saved session if the entire trajectory was read in before saving
  • Measure and Color Blobs (Surface/Binding Analysis, Volume Data) —
    • can generate a new color for each blob
    • can draw bounding box aligned with principal axes of inertia
  • Minimize Structure (Structure Editing) — can remember settings of secondary dialogs (Dock Prep etc.) for optional use in subsequent minimizations
  • Model Panel (General Controls) — added biological unit and Ramachandran plot functions
  • Movie Recorder (Utilities) — variable bit rate encoding (Q=8) now default
  • Multalign Viewer (Sequence) —
    • Blast protein search available from Tools menu
    • trees saved in sessions
    • single-sequence files can be read/written
    • can read alignments (only) from HSSP files
    • vertical scrolling with mouse scroll wheel
    • can add sequence(s) from a file (previously just from structure or pasted as plain test)
    • alignment headers may contain symbols (circle, square, diamond, star)
  • Phantom Force Feedback (Volume Data) — removed
  • Render by Attribute (Depiction, Structure Analysis) — for convenience in setting colors, added built-in palettes and the ability to reverse color order with a single click
  • ResProp (Structure Analysis) — coloring section removed
  • Rotamers (Structure Editing) — the existing sidechains can be retained
  • Surfnet (Surface/Binding Analysis) — simplified into a single dialog without loss of functionality
  • Thermal Ellipsoids (Structure Analysis) —
    • anisotropic B-factors read from CIF/mmCIF (previously only PDB)
    • depictions saved in sessions
    • possible depictions include ellipsoid principal axes and/or principal ellipses in addition to the ellipsoids themselves
    • includes Presets menu for rapid access to predefined combinations of options
  • Transform Coordinates (Movement) — renamed from Transform Molecule Coordinates, now works on all model types
  • Volume Filter (Volume Data) —
    • Gaussian filtering more memory-efficient, allows specifying output value type
    • added Flatten filter
New Commands:
  • coulombic — command-line implementation of Coulombic Surface Coloring
  • lighting — adjust lighting and shininess
Command Changes:
  • 2dlabels
    • includes 2D arrows in any orientation
    • 2D labels including text, symbols, and arrows can be written to and read from files (allows transferring labels between sessions, hand-editing, saving labels without saving the entire session, etc.)
  • align — can align an axis or plane object (previously worked only on atoms)
  • angle — can measure angles between axes and/or planes
  • aniso — added options for display of thermal ellipsoid principal axes and/or principal ellipses, other changes as listed above for Thermal Ellipsoids
  • close — more than one model number can be given
  • define — can calculate centroids (previously just axes and planes)
  • distance — can measure distances involving axes, planes, and/or centroids
  • findclash — allows checking for interactions between two independently specified sets of atoms (not just a specified set against itself or all other atoms)
  • findhbond (hbonds) — allows finding only those H-bonds between the selection and an independently designated set of atoms; pseudobonds drawn to hydrogens if present instead of donor heavy atoms
  • help — use without arguments opens the search dialog
  • measure — added spine calculation of a path along the center line of a segmentation region from Segment Map
  • morph — added nogui true option to suppress MD Movie dialog
  • movie
    • variable bit rate encoding (Q=8) now default
    • new crossfade option for transition by linear interpolation
  • nucleotides — added ~nucleotides for convenience (equivalent to nuc side atoms)
  • rock, roll, turn — a center of rotation method can be specified just for executing the command (for example, allows rotating around the center of view with the command even if a different center is used for rotation with the mouse)
  • setattr — added M flag, all applicable models
  • shape — can generate ellipsoids, rectangles, flat ribbons, apply specified rotations to some shapes
  • swapaa — the existing sidechains can be retained
  • sym — option to generate low-res surfaces instead of atomic copies for efficiency on large systems
  • vop — added flatten and unbend operations, gaussian allows specifying output value type
  • redundant commands removed: load, source, rescolor, resrepr, x3dsave, brotation, push, pop
Notable Bugfixes:
  • transparent ribbons no longer contain extraneous disks
  • eliminated blocky artifacts that could occur around labels in a scene with transparency
  • when possible, shadows are smoother
  • shadows and labels can be used at the same time
  • saving images now uses OpenGL framebuffer objects for off-screen rendering to work around problems with some platforms (mostly older Macs and some Linux systems)
Known Bugs:
  • surfaces fail for some structures
  • POV-Ray incorrectly renders some of the characters in the fonts Chimera uses, especially the zero
  • the inside ribbon color is not exported (e.g., POV-ray does not show it)
  • Gromacs trajectories from version 4.5.1 (and later) do not work. Version 4.0.2 (and earlier) trajectories do work. The status of intermediate trajectory versions is unknown at this time.
  • Mac OS X problems:
    • in Mac OS X 10.6.4, the display of large surfaces (> 15 million triangles) can cause the machine to freeze requiring a reboot. This is a graphics driver bug effecting both Nvidia and ATI graphics cards.
    • in Mac OS X 10.5, opening and then closing IDLE adds the IDLE menus to the Chimera menus, and trying to use the extra menus generates errors
    • in sequential stereo, the drag selection outline is only visible for a fraction of a second when the mouse button is released
  • Mac OS X with X Windows problems:
    • Observed with 10.5 (Leopard):
      • sometimes display does not update (can be forced by slightly moving the view contents with the mouse)
      • sometimes saved images have a corrupt or "mis-tiled" appearance. Workarounds to try include:
        • showing the Command Line if it is not shown (or if it is shown, hiding it) and then re-saving the image
        • saving the position with command savepos, jiggling the view with the mouse, restoring the position with reset, and then re-saving the image
        • saving a session, then using the native Mac version of Chimera (non-X11) to restore the session and re-save the image
    • Observed with 10.6 (Snow Leopard):
      • Side View may come up blank, but will be filled in when structures are moved
      • closing the Viewing dialog (Side View, Lighting, etc.) causes chimera to crash on next graphics redraw

v1.4.1 [02-23-10]

Appearance and Image-Saving:

  • nicer initial default display (New Molecules

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