Chimera

Licence: Other Open Source
Version 1.4 | Release Date: 2009-10-01 | Download

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
new blast protein function in the Model Panel uses a 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
Pub3D fetching and SMILES→3D 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)
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
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
New Tutorials:

Density Display image tutorial
Similar Binding Sites image tutorial
B-Factor Coloring image tutorial
Major Bugs Fixed:

interpolation between saved positions by reset corrected to better preserve the relative orientations of models as they move
the color menu in the Mac Aqua version now shows colors (not just their names) and has two columns
Known Bugs:

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
surfaces fail for some structures
POV-Ray incorrectly renders some of the characters in the fonts Chimera uses, especially the zero

Version 1.0.2470 | Release Date: 2008-04-05 | Download
No changes specified