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UCSF Chimera Updated

A new production release of UCSF Chimera (version 1.4) is now available. Download is free for noncommercial use. The download includes full documentation and tutorials.

Many improvements and new features have been added since the previous production release (Dec 2008), as listed in the release notes:
http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.4.html

Changes since the previous production release (1.3):
Appearance and Image-Saving:
  • nicer initial default display (New Molecules "smart" preference, similar to ribbons preset; can be turned off to give the previous behavior, or circumvented with command open noprefs)
  • default ribbon style changed to rounded (New Molecules preference)
  • CA-only and P-only structures can be shown as ribbons and worms
  • ribbons preset includes special nucleotide representations, hides hydrogens on carbon atoms
  • default nucleic acid ribbon rotated 90° from the previous default
  • improved transparent surface appearance (single-layer and angle-dependence options, can be combined with silhouette edges)
  • quality option in Lighting tool turns on glossy lighting and angle-dependent transparency (grayed out if your graphics driver is not capable)
  • BILD objects can be made transparent (thanks to David Beck, University of Washington)
  • images now rendered offscreen on most platforms (not supported by X11 in Mac OS or by certain older machines with other operating systems)
  • raytracing:
    • global clipping included
    • improved translation of transparent colors from Chimera to POV-Ray
    • defaults changed: increased antialias threshold (faster rendering), no jitter (better movie appearance)
  • added row-interleaved stereo mode in Camera tool for use with displays from VRex, Miracube, Zalman, and others
I/O:
  • new Fetch preferences allow specifying a download directory, later using local copies of the data (when available)
  • added fetch types EMDB and EMDB & fit PDBs
  • Fetch by ID allows keyword search of EMDB
  • Pub3D fetching and SMILES3D conversion updated to use the new REST services provided by the Chembiogrid (CICC) at Indiana University
  • output TIFF images now LZW-compressed (uncompressed available as "TIFF-fast")
  • added output image format PPM
  • added export format STL (binary, triangle-based)
  • added New Molecules preference to control naming of models read from Mol2 files
  • sessions saved with this release are much more memory efficient as they are being restored (but approximately the same memory use after restoration is complete)
  • session files containing surfaces are smaller
  • exported X3D files now default to version 3.0, unless version 3.2 features are needed (e.g., clip planes, orthographic viewpoints), so more X3D browsers and converters can understand the files
General:
  • new front center rotation method is the default
  • clipping is off by default (front/back planes automatically adjust to avoid clipping anything) but can be turned on by moving the planes or focusing on specific items
  • center of rotation rather than camera center used for zooming with the mouse or the scale command
  • labels can be repositioned with the mouse (default Ctrl-right button)
  • amino acid phi, psi, chiN angles automatically assigned as attributes and can be changed with setattr or in the Selection Inspector
  • new preferences: initial window size, how often to check for updates
  • Matplotlib included in distribution
  • on Macs, all file types can be opened by drag-and-drop on the Chimera icon, not just PDB and Chimera Web data
  • on Mac Aqua, click-through has been implemented and the "window focus follows mouse" preference removed
  • can read double-precision DelPhi maps produced by some versions of the Intel Mac executable from the Honig lab
  • 3Dconnexion SpaceNavigatorTM input device supported on Linux (thanks to Thomas Margraf, University of Hamburg)
New Tools:
  • Add Ions (Structure Editing, Amber) — add counterions using AmberTools (thanks to Wei Zhang, The University of Texas Health Science Center at Houston)
  • Blast Protein (Sequence) — perform protein sequence searches using a BLAST Web service hosted by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI); the pseudoalignment from BLAST can be shown in Multalign Viewer, and any corresponding structures can be fetched and superimposed
  • Coulombic Surface Coloring (Surface/Binding Analysis) — color molecular surfaces by Coulombic electrostatic potential (see http://tinyurl.com/mzopva for an informal comparison with published figures of Poisson-Boltzmann electrostatic potential)
  • Hide Dust (Volume Data) — hide small disconnected bits of a surface
  • Task Panel (General Controls) — interface to jobs started by Chimera
  • Thermal Ellipsoids (Structure Analysis) — show anisotropic B-factors
Tool Changes:
  • 2D Labels and Color Key (Utilities) —
    • added font style/typeface options
    • checkboxes allow showing/hiding individual 2D labels
  • Add Charge (Structure Analysis, Structure Editing) — charge methods for nonstandard residues shown on initial dialog
  • Axes/Planes (formerly Axes) (Structure Analysis) —
    • axis radii can be set to the average axis-atom distances
    • axis colors shown in color wells, can be changed
    • planes can be defined, displayed as disks, included in measurements
  • Build Structure (Structure Editing) — secondary dialog allows more convenient specification of peptide phi/psi angles
  • Dock Prep (Structure Editing) — added options for changing modified RNA residues 5BU, CSL, UMS to the corresponding standard residues
  • Effects (Viewing Controls) — depth cueing yon intensity parameter replaced with end parameter for greater control when clipping is off
  • Fit in Map (Volume Data) —
    • Undo/Redo capability added
    • map-map correlation can be optimized
    • movement can be restricted to selected atoms only (previously the entire models containing the atoms were moved as rigid bodies)
  • Icosahedron Surface (Higher-Order Structure) — status saved in sessions
  • Lens Inspector (Depiction) removed
  • MatchMaker (Structure Comparison) — added option to call Match -> Align after superposition to create a structure-based alignment
  • Match -> Align (Structure Comparison, Sequence) —
    • RMSDs over fully populated columns of the sequence alignment reported in Reply Log
    • can iterate refitting the structures using the sequence alignment and generating a new sequence alignment from the new superposition
  • MD Movie (MD/Ensemble Analysis) —
    • added support for Gromacs 4 trajectories
    • Amber residue names remapped to standard PDB residue names for better integration with other tools (Rotamers, Nucleotides, Sequence, etc.)
  • Model Panel (General Controls) —
    • columns reordered, narrowed by shortening Active and Shown to A and S
    • arbitrary notes can be created and shown as a column
    • models can be renamed
  • Movement Mouse Mode (Movement) — added option to move entire molecule model under cursor
  • Multalign Viewer (aka Sequence) —
    • Preferences reorganized, includes separate Appearance settings for multiple alignments and single sequences
    • allows copying a sequence as plain text so it can be pasted into another application window
    • Sequence includes any residues not in the structure itself but in SEQRES records in the input structure file
    • moved to new tools category Sequence
  • Nucleotides (Depiction) —
    • new ladder display and associated parameters
    • interface reorganized, defaults changed
    • representation colors automatically update to match atoms
    • representations saved in sessions
  • Reply Log (Utilities) — text-copying and string-searching added to dialog
  • Surface Color (Volume Data) —
    • coloring by volume data has per-pixel option
    • coloring by electrostatic potential uses surface offset
  • Transform Molecule Coordinates (Movement) — added buttons to Reset (restore original coordinates) and Set (equivalent to reset + apply)
  • Unit Cell (Higher-Order Structure) — can make blocks of multiple unit cells
  • Volume Filter (Volume Data) —
    • renamed from Gaussian Filter
    • additional options for binning, smoothing, shifting, scaling data
  • Volume Tracer (Volume Data) —
    • markers placed in successive residues for easier command-line specification
    • added option to place markers on surfaces
  • Volume Viewer (Volume Data) —
    • outline box linewidth can be adjusted
    • initial thresholds for signed data are placed symmetrically about zero
    • region autodisplay setting moved from Data display options to Subregion selection
New Commands:
  • aniso — show thermal ellipsoids
  • aromatic — show ring aromaticity
  • coordset — play through frames of a trajectory
  • define — calculate axes, planes for sets of atoms
  • fillring — show rings as filled
  • fly — smoothly traverse a series of saved positions
  • mcopy — copy settings (colors, display styles, etc.) from one molecule model to another
  • measure — perform several calculations on structures, surfaces, and maps (relative transformation, surface area, enclosed volume, map-map correlation, inertia ellipsoid, etc.)
  • nucleotides — create special nucleotide representations (command implementation of Nucleotides tool)
  • pause — suspend command script execution until the user presses a key
  • runscript — run Python script with command-line arguments
  • scolor — color surfaces a single color or by volume data or geometry (command implementation of Surface Color)
  • sop — edit a surface model
  • tile — arrange models in a plane
  • windoworigin — set graphics window location
Command Changes:
  • command script execution can be aborted with Esc, or paused/resumed with Shift-Esc
  • commas in command-line atom specifications imply ordering (previously, comma-separated models, residues, or atoms were not necessarily used in the order in which they were typed)
  • more commands allow colors to be specified with Tk codes (e.g., #ff00ff) or R,G,B[,A] tuples
  • 2dlabels — added font style/typeface options
  • addcharge — default charge set changed to ff99SB
  • cofr — fixed center of rotation can be specified in the coordinate system of a reference model; syntax improvements, access to all center of rotation methods
  • focus — added ~focus (equivalent to focus without arguments)
  • label, rlabel — label offset can be specified
  • mask — can invert mask to get the opposite data
  • match — added options to suppress the transformation, report the matrix
  • matrixcopy — multiple target models can be specified
  • move — translation direction can be specified in the coordinate system of a reference model; specified models move regardless of whether they are active
  • rangecolor — added option to call Color Key
  • reset — models not present when the position was saved now transform along with the lowest-ID model that was present
  • rock, roll, turn — rotation axis and center can be specified in the coordinate system of a reference model; specified models move regardless of whether they are active
  • rotation — can specify torsion ID, adjust torsions (rotate bonds), deactivate torsions
  • set — expanded to control depth-cueing, silhouette edges, subdivision quality, projection mode, lighting quality
  • setattr — expanded to control molecular surface attributes
  • shape
    • location (center) can be specified with x,y,z coordinates or a set of atoms
    • slab option added
    • cylinders can be capped
    • can make a tube connecting a series of atoms or markers (à la Volume Tracer)
  • surftransparency — expanded to nonmolecular surfaces; frame argument added for movie scripting
  • sym — cyclic, dihedral, icosahedral, helical, and translational symmetries can be specified (previously only BIOMT records were used)
  • volume
    • added planes playback for scripting animations
    • file-saving allows step, subregion specification, saving multiple files at once
  • vop
    • added several types of filtering, binning, scaling, axis permutation, subregion (box) extraction, periodic map extension, map addition, morphing
    • subtraction improved to automatically resample as needed, use specified scale factors
  • redundant commands deprecated: load, source, ribcolor, x3dsave, brotation, push, pop
Known Bugs:
  • in Mac Aqua Chimera, trying to access the menu while a background job (e.g. Blast search) is running causes a hang. A 1.4.1 release that fixes this problem is planned. In the meanwhile, multiple-iteration blast searches (psiblast) and blasting against nr are disabled in the Mac Aqua version only.
  • Mac OS 10.5 / X11 problems:
    • 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, restoring the session in the Mac Aqua version of Chimera, and then re-saving the image
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