Contents
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)
- avoid crashes and reduce memory use when saving ribbon images by not subdividing as much — if you notice a difference, use the Effects tool to increase the subdivision quality as needed
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)
- Mac OS X problems:
- in Mac OS X 10.6 Chimera sometimes crashes in the Mac OpenGL driver when saving images or zooming in on molecule ribbons or when displaying large surfaces.
- 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. This appears to be fixed in Mac OS 10.6.5.
- 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