The Coot Team are pleased to announce the release of Coot-0.5 Ueno.
source: http://www.ysbl.york.ac.uk/~emsley/software/coot-0.5.tar.gz binaries: http://www.ysbl.york.ac.uk/~emsley/software/binaries/stable (binaries for other platforms will be appearing in due course). Paul. ---- Release 0.5 Ueno o FEATURE: Coot now has a Preferences dialog. o FEATURE: Coot now is PDB version 3.0 compliant. o FEATURE: Additional Representations added [Tadeusz Skarzynski]. o FEATURE: "Fixed Atoms" for refinement have been introduced. o FEATURE: Monomer restraints can be edited in a GUI and are exported to the scripting layer. o FEATURE: Coot can now make difference maps. o FEATURE: The state file now remembers the refinement map number [Herb Klei]. o FEATURE: Add dialog position preferences to Extensions. o FEATURE: The state file now remembers the scroll-wheel (contour changing) map [Kevin Madauss]. o FEATURE: Add a variable reduce-molecule-updates-current, that when set by the user causes an update of the probed molecule, not the generation of a new one [Bob Nolte]. o FEATURE: Add Terminal Residue now assigns the correct residue type (if a PIR sequence has been given for side-chain docking) [Bob Nolte]. o FEATURE: "Pukka Puckers?" validation tool for RNA. Based on Davis et al. (2007) Molprobity: all atom contacts and structure validation for proteins and nucleic acids, Nucleic Acids Research 35, W375-W383. o FEATURE: "Active site" hilighting. Cheep and cheerful solid modelling of ligand and neighbouring residues [Herb Klei]. o FEATURE: Double-clicking on an atom labels it (CCP4mg compatibility). o FEATURE: "Eigen-flip" function added. Use to quickly flip around ligands. o FEATURE: it is now possible to add a setting so that atoms with zero occupancy are not moved when refining: set-refinement-move-atoms-with-zero-occupancy [Rajiv Chopra] o FEATURE: Refmac can be run from Coot without the user having to explicitly set the column labels. o FEATURE: NCS Copy Chain is now available as a GUI extension. o FEATURE: The ability to turn on chi angles that move hydrogens is now available from the Chi Angles dialog. o FEATURE: The "About" dialog contains references. o CHANGE: Key bindings mechanism has changed. Now we are able to display key binding in a GUI widget. o CHANGE: Molprobity Tools (probe and reduce) will only now work with those binaries that are hybrid_36 enabled. o CHANGE: Picking has been changed to somewhat favour those atoms at the front of the slab. o CHANGE: When deleting a residue while displaying validation graphs, the graphs get updated immediately [JED] o CHANGE: In CA display mode, only CAs can now be picked. o CHANGE: Nudge centre axes are now relative to the screen rather than in world coordinates. o CHANGE: NCS skipping changed. Hopefully faster now [Steven Sheriff]. Also works in the case of hetero dimers with NCS [Phil Evans]. o CHANGE: default bond width changed to 5. o CHANGE: Traffic lights verticalized. o CHANGE: Symmetry colour info added to state file [Doug Kuntz]. o CHANGE: the argument order for "mutate" scripting function have been canonicalised. o CHANGE: set-symmetry-colour-merge now takes only a fraction argument. o CHANGE: Mutate no longer changes the atom order in the pdb file. o CHANGE: Next Residue/Previous residue reworked so that it now jumps over gaps and goes to the right residue when encountering insertion codes. o CHANGE: Don't allow translation drag of intermediate atoms during rotamer selection. o CHANGE: Reference structures now have strand markup in the header, so they can now be used as the reference structures for "Build Strand". o CHANGE: Bond parameters changes (bond width and hydrogens state) now work immediately, no need to press the "Apply" button [FvD]. o CHANGE: Colour by Chain style also now displays zero occupancy markers [PRE]. o CHANGE: Modelling toolbar can now be removed or docked in different positions. o BUG-FIX: chiral volumes are now correctly handled for multiple monomer bespoke ligand dictionaries. o BUG-FIX: Hydrogens names are better handled after an undo operation - no longer do they fly off when refining [Joel Bard] o BUG-FIX: Non-flexible ligands can be added to ligand search when the "flexible?" option is selected. Previously the ligand search was aborted. o BUG-FIX: Flexible ligand fitting when the torsion period is 0 and for ligands that have bonding defined from a cif file (no atom left behind). o BUG-FIX: side-by-side stereo mode improved [Randy Read]. o BUG-FIX: Now coot does not crash on when displaying NPD atoms in anisotropic representation [Mitch Miller]. o BUG-FIX: Now coot does not crash when opening "Cell & Symmetry" with no molecules loaded. o BUG-FIX: Coot no longer crashes when deleting a residue with an Alt Conf [JED]. o BUG-FIX: Coot can now do rotamers on a MSE residue [Mark Saper] o BUG-FIX: Can now read SHELXL .ins files with lowercase symops. o BUG-FIX: On additions to a SHELXL molecule: better handling of UNIT and SFAC cards [GMS]. o BUG-FIX: EQUIV cards from SHELXL handled better. o BUG-FIX: Adding waters to a SHELXL molecule now adds them with default occupancy 11.0 [Tobias Beck] o BUG-FIX: Go To Atom dialog is properly updated on merging molecules. o BUG-FIX: Coot no longer crashes when opening the Bond Parameters dialog before a pdb file has been read. o BUG-FIX: NCS Loop function now properly mutates residues in the peer chains [PRE]. o BUG-FIX: Add Terminal Residue deletes the TER record (if it existed) of previous C-terminus [PRE]. o BUG-FIX: Povray output improved. o BUG-FIX: The representation is no longer changed after editing atoms in CA+ligs representation. -----
