[Chimera-users] release candidate

Eric Pettersen pett at cgl.ucsf.edu
Tue Sep 20 18:32:35 PDT 2005

So we've put a release candidate on the download page (http:// 
www.cgl.ucsf.edu/chimera/download.html).  We're hoping that if you  
have the time, you'll download it and bang on it and let us know  
about any bugs you find before it turns into a production release.

It's been a _long_ time since the previous production release  
(December of last year).  Here are the major highlights:

-> selections can be inverted (Select menu, "select" command, arrow  
-> additional arrow key functions:
     left: undo selection
     shift-left: clear selection
     right: invert selection in models with selections
     shift-right: invert selection in all models
-> PDB file writing can be restricted to displayed and/or selected atoms
-> Chimera scene can be exported (formats: X3D, POV-Ray, Renderman,  
VRML [latter surfaces only])
-> Actions...Set Pivot sets center of rotation w/o zooming
-> Help...Search Documentation searches local documentation
-> Tools menu reorganized
-> balloon help over bonds/pseudobonds includes length
-> residue labels now positioned at centroid of displayed atoms
-> new residue attribute "isHet" (whether residue is in HETATM PDB  
-> nucleic-acid ambiguity codes can be used in subsequence searching  
(R=A/G, Y=C/T/U, N=A/C/G/T/U)
-> switched to Python 2.4

New Tools
-> Attribute Calculator (Structure Analysis):  generate new numerical  
attributes from existing ones; calculate totals or averages of an  
-> Color Zone (Volume Data):  color surface patches near selected  
atoms with those atoms' colors [for GRASP surfaces and Volume Viewer/ 
Multiscale surfaces rather than standard molecular surfaces]
-> Demo Editor (Demos):  graphical interface for creating demos
-> Movie Recorder (Utilities):  capture image frames from Chimera and  
assemble them into a movie file
-> Surface Capping (Depiction):  cap surfaces where they intersect a  
clipping plane (giving the illusion of the surface as a solid object  
rather than a hollow object)
-> Surface Color (Volume Data):  color surfaces according to volume  
data or geometry (distance from a point, plane, or axis)
-> Electrostatic Surface Coloring (Surface/Binding Analysis):   
specialization of preceding tool to facilitate coloring with  
electrostatic volume data;  also replaces DelphiViewer
-> Surface Zone (Surface/Binding Analysis):  restrict GRASP or  
Multiscale Models surface display to zone around selected atoms
-> Values at Atom Positions (Volume Data):  map volume data to atom  
positions;  create atom attributes with the values
-> 2D Labels (Utilities):  create arbitrary text labels and place  
them in 2D

Tool Changes
-> Benchmark (Utilities):  now also benchmarks molecule display  
-> Demos (Demos):  new Hormone-Receptor Complex demo
-> Lighting (Viewing Controls):  new simplified interface available
-> MatchMaker (Structure Comparison):  can include secondary- 
structure term in the alignment score and can iterate the fit
-> MD Movie (formerly Movie; Utilities):  new "md:" prefix for  
metafiles; add step size option for playback; RMSD map calculation  
speeded up; can automatically recolor RMSD map for contrast; ability  
to collect atom occupancy data and display it with Volume Viewer;  
user-friendly interface to Movie Recorder for generating movie from  
-> MultAlign Viewer (Structure Comparison):  all-gap positions can be  
omitted from saved files; all headers available as residue attributes  
in associated structures; more sophisticated conservation measures  
available (calculated with AL2CO program); headers can be saved to a  
file or loaded from a file; structure association info can be saved  
to a file
-> Multiscale Models (Higher-Order Structure):  separate surfacing  
threshold for CA-only chains
-> Nucleotides (Depiction):  now assigns a pucker value to all sugar  
atoms (plane/envelope/endo/exo)
-> Per-Model Clipping (Depiction):  new slab mode to show just a  
slice of a model
-> ViewDock (Surface/Binding Analysis):  saves in sessions;  H-bond  
statistics can included in the columns of ligand descriptors (and  
used for sorting)
-> Volume Viewer (Volume Data):  major interface reorganization;  
added support for UHBD electrostatic potential (binary only),  
gOpenMol, and PROFEC grid formats;  support added for non-orthogonal  
crystal data

New Commands
-> 2dlabels:  command-line version of 2D Labels tool
-> movie:  command-line version of Movie Recorder tool
-> writesel:  command-line version of Actions...Write List

Command Changes
-> color:  can now also color ribbons
-> British spellings added for gray, color, and center
-> match:  added "iterate" keyword to allow pruning bad pairs until  
worst pair is below a threshold
-> matchmaker (mmaker):  added keywords corresponding to new  
MatchMaker tool abilities
-> select:  new keyword for inverting selections
-> write: keywords for restricting to displayed/selected atoms

-> new Attributes tutorial:  covers Render by Attribute, Surface Area/ 
Volume, Attribute Calculator, and advanced command-line usage

full release notes are at:  http://www.cgl.ucsf.edu/chimera/docs/ 

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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