Dear All, We are pleased to announce the release of Coot 0.6.2.
You can find the binaries here: http://lmb.bioch.ox.ac.uk/coot/software/binaries/releases/ http://www.ysbl.york.ac.uk/~emsley/software/binaries/stable/ http://www.ysbl.york.ac.uk/~lohkamp/software/binaries/stable/ For Mac builds, we'll have to wait for Bill Scott. (For clarity, release 0.6.2 does not contain the 2D ligand gui.) Thanks for your patience, The Coot Development Team. Release 0.6.2 o FEATURE: PISA Interfaces can now be represented in Coot (requires pisa version 1.06 or later). o FEATURE: Regularize sphere function introduced. o FEATURE: --update-self to update pre-release binary from server. o FEATURE: SBase molecules can be imported (under Search Monomer Library). o FEATURE: prodrg-ify ligand function added (generates restraints for the specified residue). o FEATURE: highly-coordinated waters metal substitution search added. o FEATURE: Rudimentary support for reading 3D MDL mol2 files. o FEATURE: New map representation styles, solid/transparent and "cut-glass". o CHANGE: Align & Mutate now provides a simple dialog with the alignment. o CHANGE: Environment distances are separated into bumps and bonds [Bob Nolte]. o CHANGE: Move molecule here only moves small molecules by default now. There is an check button to allow big molecules [Kevin Madauss]. o CHANGE: In MTZ reading Expert Mode, if the low resolution limit is not set, then presume that it was 999.9A [Randy Read]. o CHANGE: Faster, multiprocessor electrostatic surfaces [Martin Noble]. o CHANGE: pointer distances are updated on go-to-blob [JED]. o CHANGE: COOT_SCHEME_EXTRA_DIR and COOT_PYTHON_EXTRAS_DIR are now ":"-separated lists [Thomas Womack]. o CHANGE: Real-space refinement is now interruptible [JED]. o CHANGE: NCS skipping now works in the reverse chain order too (Shift-O) [JED]. o CHANGE: Residues are checked atom by atom against the dictionary and refinement is not started if there is not complete agreement (for non-Hydrogen atoms) [JED]. o CHANGE: Merged molecules are undisplayed after merging. o CHANGE: "Replace residue" will use a dictionary and model for a particular 3-letter code if they have been already read in (rather than run libcheck blindly) [Ian Tickle]. o CHANGE: SSM overlayed molecule now takes symmetry of reference molecule o CHANGE: Waters are now represented with "~" in the sequence view - so that there is a distinction between waters and interesting hetatoms. o CHANGE: Using the scroll wheel with Ctrl and Shift will change the representation of the molecule that has the active residue. o CHANGE: difference_map_peaks() function now takes an addition argument specifying the minimum distance between peak (filtering out close smaller peaks). o CHANGE: Waters are not considered when calculating the clash score during rotamer fit. o BUG-FIX:: Hydrogens on waters are no longer checked against the difference map in the water validation test. o BUG-FIX: Water search now avoids close contacts to waters generated in the same round. o BUG-FIX: Water check in gtk1 version no longer tries to dereference the difference map active checkbutton - fixes crash [Subhangi Ghosh]. o BUG-FIX: Fix crash on rigid-body refine by atom selection with residue gaps [Joel Bard]. o BUG-FIX: rename residue works on only the specified chain. o BUG-FIX: anomalous maps are now properly recovered from the state file [Phil Evans]. o BUG-FIX: Symmetry is updated on accepting a Rotate/Translate modification [Ezra Peisach]. o BUG-FIX: NCS differences were broken by gaps of different lengths [Ingo Korndoerfer]. o BUG-FIX: Unconventionally formatted atom tree records in restraints cif now no longer cause a crash when using Chi Angles [JED]. o BUG-FIX: Fix the crash when sphere refine was used at the same time that the geometry graph was displayed [JED]. o BUG-FIX: rotate/translate large fragments now works better. o BUG-FIX: transform-map function fixed for 5 arguments. o BUG-FIX: Sort-chains no longer loses header information [Bob Nolte]. o BUG-FIX: Environment distances are no longer drawn between atoms with differing non-blank alt-confs. o BUG-FIX: mmCIF file writing fixed. o BUG-FIX: Zero occupancy marker on hydrogens are not undisplayed properly [JED]. o BUG-FIX: refining with structures from .res files sometimes crash when writing backup file on Mac [Derek Logan]. o BUG-FIX: Rotating/translating ligands in CA+Ligands mode now works [Jim Thorpe]. o BUG-FIX: Platinum can now have sensible bonds to N and O [John Helliwell]. o BUG-FIX: Ramachandran plots work at the end of chains chains with missing residues [JED]. o BUG-FIX: Environment distances display toggling anomalies cleaned up [Ed Pozharski]. o BUG-FIX: Sequence view failed with SHELX molecules with high residue numbers [Stefan Becker]. o BUG-FIX: SSM superposition now superposes the correct molecules when the option menus are not adjusted [Sam Stampfter].
