News

Mole

v2.13.9.6 (6.9.2013)

• UI: Fixed a bug with molecular surface display when changing parameters.
• UI: Added Cavity Details window.

v2.13.8.26 (26.8.2013)

• Lining residues of cavities are now exported in cavities.xml.
• Computation of physico-chemical properties of cavities.

SiteBinder

v2.0.14.1.14 (14.1.2014)

• Added an upper limit to how many combinations can be tried when superimposing two structures.

v2.0.14.1.11 (11.1.2014)

• Fixed a pairing bug that surfaced after fixing the RMSD bug.

v2.0.14.1.10 (10.1.2014)

• Fixed a RMSD calculation bug.

v2.13.11.29 (29.11.2013)

• The superimposing algorithm now runs in parallel on the structure level. As a result, when superimposing large number of structures, the algorithm should be up to several times faster.

v2.13.11.24 (24.11.2013)

• Made large changes to the superimposition algorithm that hopefully improve the overall results. The side effect is that for larger structures (with high degree of atom bonds), the algorithm is slower.

v2.13.8.6 (8.6.2013)

• Average structure is now being exported using the "Export -> CSV Info and Superimposed" function.

v2.13.7.29 (29.7.2013)

• Fixed a bug where structures could not sometimes be superimposed if all atoms were not selected.

v2.13.7.15 (15.7.2013)

• Made improvements to the superimposition algorithm.

v2.13.7.4 (4.7.2013)

• Result export now correctly exports only selected entries.

v2.13.5.22 (22.5.2013)

• An option to group structures by selected atoms.
• Fixed a bug in the Combinatorial method that made it slower than it should be.

v2.13.4.13 (13.4.2013)

• It is now possible to choose descriptor columns to be exported.

v2.13.4.12 (12.4.2013)

• Ability to set how many structures to display.
• Fixed the "T" button and it should behave more "naturally".
• Added a function to cluster motives based on their residues.

Charges

v1.0.14.1.27 (27.1.2013)

• Changed how the total charge is handles when using the cutoff method - for each atom, the total charge is weighted by the <amount of atoms in radius>/<total number of atoms>.

v1.13.6.26 (26.6.2013)

• Bug fix: Pearson coefficient wasn't squared.

v1.13.5.26 (26.5.2013)

• Support for the PQR file format.
• Reference charges can now be also loaded from Mol2 and PQR files (i.e. load a PDB file and use Mol2 or PQR file to load ref. charges).

v1.13.5.23 (23.5.2013)

• Comparison of "aggregate charges".

v1.13.5.19 (19.5.2013)

• Grouping of atoms into residues and other "sub-structures" and computing charges on these.
• Computation of "aggregate charges".
• 3D visualization.

MotiveQuery

1.11.2013

• Added function ResidueIds.

23.10.2013

• Added functions IsConnected, CommonAtoms, AminoSequenceString.

21.10.2013

• Added functions Star and Path.

15.7.2013

• Added the MQ.Execute function.

7.6.2013

• Added ChargeType option AminoAcids function.

30.5.2013

• Added function Filled.

23.5.2013

• Changed the name of function RegularMotive to RegularMotives.
• Changed the order of arguments to make them more consistent for "function versions" (the ones without .) of these functions: ConnectedAtoms, ConnectedResidues, AmbientAtoms, AmbientResidues, Count, Find, AtomProperty, Descriptor. Refer to MotiveQuery Language Reference.

General

16.3.2014

• Added basic support for PDBx/mmCIF format.

13.1.2014

• PDB exports now include all CONECT records.

26.5.2013

• Support for the PQR file format (should work in all apps, except Mole 2.0).