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CCP4BB  December 2009

CCP4BB December 2009

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Subject:

Coot 0.6 Released

From:

Paul Emsley <[log in to unmask]>

Reply-To:

Paul Emsley <[log in to unmask]>

Date:

Wed, 9 Dec 2009 22:48:01 +0000

Content-Type:

text/plain

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We are please to announce the release of Coot-0.6 (including WinCoot)

Source here:

http://www.biop.ox.ac.uk/coot/software/source/releases/coot-0.6.tar.gz

Binaries from here:

http://www.biop.ox.ac.uk/coot/software/binaries/releases/

Paul.

p.s. Sorry for the cross-posting, but it is apparent that a good number of Coot users are not on the Coot list.


----------

  Release 0.6

  o FEATURE: User-defined clicks [Joel Bard].

  o FEATURE: SHELXL interfaces allows the user to modify the input before
    running the SHELXL executable [Tobias Beck].

  o FEATURE: Now compatible with Zalman M220W.

  o FEATURE: Post-manipulation function hook added [JED].

  o FEATURE: "Sphere" (residue selection) refinement.

  o FEATURE: function to (re-)calculate probe dots around a give point
    [Joel Bard].

  o FEATURE: monomer and residue selection dipoles.

  o FEATURE: Interactive map sharpening [Randy Read, Alex Brunger].

  o FEATURE: LINK bonds are are now represented.

  o FEATURE: "Backrub rotamers" at low (2.7 or worse) resolution.

  o FEATURE: Baton build parameters (e.g. "backwards") now have a GUI
    [Phil Evans].

  o FEATURE: Move waters to surround protein [Garib Murshudov]

  o FEATURE: rotate/translate zone by residue ranges

  o FEATURE: Rigid-body fit by residue ranges.

  o FEATURE: Multi-select on reading coordinates is enabled.

  o FEATURE: Immediate access to coordinates from CIF dictionaries
    that contain coordinates (no need for LIBCHECK in such cases).

  o FEATURE: Nudge-residue (bound to Ctrl-arrow keys).

  o FEATURE: A dialog has been added from map averaging [Bob Nolte].

  o FEATURE: Rename residue [Alexander Schiffer].

  o CHANGE: partial charges added to electrostatic surface calculation.

  o CHANGE: shift-click and ctrl-click in the file selectors now work
    for reading in several coordinates files [Roberto Steiner].

  o CHANGE: SEGIDs are more intelligently inherited [Steven Sheriff,
    Bob Nolte].
 
  o CHANGE: Transformed make take the cell and symmetry of the
    reference coordinates.

  o CHANGE: Transformed maps take on the cell and spacegroup of the
    reference coordinates.

  o CHANGE: Coordinates Molecules transformed by LSQ take on the cell
    and spacegroup of the reference coordinates.

  o CHANGE: Pukka-puckers? fixed and re-enabled.

  o CHANGE: Ramachandran Plots now have molecule name labels [Wendy Offen].

  o CHANGE: The save coordinates dialogs active item is the first
    molecule with unsaved changes (rather than simply the first
    molecule) [Herb Klei]

  o CHANGE: "Go To Blob" now goes to the front blob, no matter what
    the density level of blobs/density behind it is [JED].

  o CHANGE: Don't display the geometry distance if the molecule
    corresponding to the start or end point is not displayed [JED].

  o CHANGE: Using the internal alignment, the weights of the affine
    gap penalty have been changed to favour mutations and larger gaps
    rather than several small gaps.

  o CHANGE: the restraints editor now uses strings
    (positive/negative/both) rather than number to represent the sign
    for chiral volumes [Andrew Leslie]

  o CHANGE: the restraints editor now adds a new entry to the
    dictionary when the comp-id is changed.

  o CHANGE: Additional representations now have an "All off" button.

  o CHANGE: Chi angles rotation now include a "reverse fragment" option.

  o CHANGE: "Add strand here" moved next to "Add Helix Here".

  o CHANGE: Convert PDB format 3.x prime atom names to star names (to
    correspond to current Refmac dictionary).

  o BUG-FIX: TER records are removed on addition of waters [Herb Klei].

  o BUG-FIX: Align vs PIR file improved [Bob Nolte]

  o BUG-FIX: Single HETATMs now are refined by rigid body (as waters
    are) when using Refine Zone.

  o BUG-FIX: new atoms (and waters) are added as HETATMs if
    appropriate [David Mathog].

  o BUG-FIX: TER records for water chains are no longer tested in
    water validation tests [Herb Klei].

  o BUG-FIX: NCS chain jumping now works on heterodimers [Jianghai Zhu].

  o BUG-FIX: The Chain Reordering function in Extensions has been fixed.

  o BUG-FIX: Torsion angle refinement convergence improved [JED].

  o BUG-FIX: Ramachandran Green spot no longer disappears on refinement.

  o BUG-FIX: Limit the sequence view canvas X parameters, so that we
    don't get X11 errors and crash [Felix Frolow].

  o BUG-FIX: Additional representations appear in both "eyes" in
    side-by-side mode.

  o BUG-FIX: Delete-atom spewing binary fixed [JED].

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