History

Changes

version 2.2.2_1

Molecule Alignment and Performance Update, Bugfixes (17.03.2014)

  • switched back to Java 6 compilation for WebStart
    • re-enabling IcedTea WebStart on Linux distributions
    • while maintaining Java 7 Update 51 compatibility
  • fixed APL@Voro issues
    • preview did not start correctly because files were not saved in the correct positions
    • GROMACS topology was not saved during PDB export if APL@Voro export was activated in the PDB settings
    • during preview, the .aplvoro file is saved now directly in the Cm2/temp director
    • during PDB saving with activated APL@Voro export, the file is saved in the directory with the name of the PDB file, just as the topology file
  • new protein/lipid alignment mode plus
    • enables to manually define the radius size in which molecules are shown in alignment mode
    • neighboring lipids as well as proteins can be shown or hidden
    • new enter dialog enables to manually change the rotation of the molecule by defining an axis angle
    • original alignment mode is still available, automatically computing the radius in which molecules are shown
    • documentation extended
  • Molecule Performance Mode added
    • to be activated in 3D Settings/Controls & Performance
    • enables to show ca. 50% more atoms in the 3D View
    • incompatible mode to the Molecule Editor as well as atom-based algorithms such as the Atom Level Minimizer
    • documentation extended
  • first improvements for heap space usage
  • fixed issues with 3D Settings dialog
    • (default) settings were partly not saved correctly
    • PPE Automatic Performance Mode is activated by default, if the MembraneEditor is installed for the first time
version 2.2.2

2D eXtreme Release (28.01.2014)

  • APL@Voro Integration
    • compatibility function for APL@Voro added in PDB Properties panel path to APL@Voro can be defined in the connection settings
    • optional Analyze Button added (it appears only if the paht was set)
    • using the Analyze function, 1) the PDB file is written and 2) the .aplvoro file which are used to directly start APL@Voro with the generated membrane (the PDBWriter searches for P - e.g. for phospholipids - or O atoms - e.g. for Cholesterol - and defines these atoms as key atoms)
    • APL@Voro compatibility information added to PDB Properties Window
    • PDB Properties Window provides now a function to write the .aplvoro file
    • new documentation: "9.6 Analysis of PDB Membrane Files with APL@Voro"
  • Membrane Packing Algorithm "The Wanderer Rookie" added
    • high-density lipid packing algorithm
    • especially feasible for membranes without proteins or rafts, if rafts or proteins should be included, it usually will be better to integrate them after the initial membrane was packed with "The Wanderer"
    • was already used in the initial MembraneEditor publication:
      Sommer et al., J Chem Inf Model 51(5):1165-1182, 2011
    • new documentation: "8.2.7 The Wanderer (Rookie)"
  • MembraneShifter Tool is now also able to shift molecules along the X/Z plane (Version 1.1)
  • extended protocol saves now all executed membrane packing algorithms, these are accessible via the menu Extras -> Show Protocol
  • Java 7 Update 51 Compatibility for Web Start Version
    • meets new Java Web Start requirements
    • tested on various Windows and Linux systems, compatible to Oracle Java 7 Update 51 and new versions of OpenJDK/OpenJRE with IcedTea (Mac OS X users, please have a look to the forum)
    • the original source code is still compatible to Java 6
    • Relocating 'libjawt.so' fix for various Linux Java versions added
  • problem with PDB model chooser in the Local Database solved
  • Membrane Packing Algorithm Interface extensions
    • added support for adding PDB files to databases (protein or lipid PDBs)
    • now it is only possible to add new entries to the database if the file does not already exist in the database
    • this.getJ3DBranchGroup() added for Java 3D experts, enabling the use of Java 3D objects in the Membrane View
    • added support for lipids with different conformations/models in the PDB file
    • during changing the models of a PDB file in the database, the PDB file is not repositioned every time in the Molecule Viewer
    • using the change-model-view, always the balls and sticks render mode is chosen
  • Extended PDB Settings
    • Residue identifier larger than 99999 can start over again with 0 instead of 1 (this strange behavior is also implemented in the original GROMACS parser, of course, the standard behavior with numbering from 1 to 99999 can still be used in all other cases)
    • the three-digit ResName of a PDB file can be used to encode the actual domain and/or layer ID to enable the tracking of these lipids
  • ScrollPane added to PDB Settings, 3D Settings, PDB Database Browser, now these dialogs are also compatible to smaller screen resolutions
  • PDBWriter bugs fixed
    • CRYST records are written correctly
    • the different transformation settings using the PDB Properties dialog are functional again
version 2.2.1_2

BGRS 2012 Release (25.06./16.07.2012)

  • support of absolute values in the component view and for the membrane packing algorithm interface (see also the remark according the MEMBRANE PACKING ALGORITHMS)
  • PPE (Protein Placing Extension) Refactoring finished
    • PDB_TM transformations are now correctly applied
      (rotations worked before, but now also the vertical alignment works fine)
    • OPM alignment method changed
      (a few proteins have had problem with the old method)
  • PDB Export Update
    • when using "Assign sequential resSeq's for each molecule" proteins are now taken into account and the Secondary Structure is maintained even if multiple proteins are exported
    • topology for GROMACS can be written to an extra file topol.top, providing the absolute number of contained lipids in dependence on the "Sort by Type or Membrane Side" option
  • the extraction of temporary files during the installation process is done now in the Cm2-folder (the old procedure caused errors on some systems)
  • membranepackingalgorithm: new functions
    • setListenerAndPrepare(MembranePackingAlgorithm algorithmToGetListeners)
    • setComputeAbsoluteValues(boolean computeAbsoluteValues)
    • setPercentages(int mode, int newval, String code, int domainID)
    • getPercentages_ExtraCellular(final int layerID, final int domainID)
    • getPercentages_IntraCellular(final int layerID, final int domainID)
    • getDecimalPlaces()
    • refreshViews(final boolean compView, final boolean memViewPanels, final boolean database, final boolean stats, final boolean props, final boolean intersections)
    • isAbsoluteValuesSelected()
  • ALL MEMBRANE PACKING ALGORITHMS HAVE TO IMPLEMENT THE FOLLOWING METHOD NOW:
    public boolean supportsAbsoluteValues() {
        return false;
    }
  • the Distributor and Random Placing algorithms are the first algorithm compatible to this method; the sub-algorithms to use can be chosen now: AddLipids, Approach, Shake, Twist; Attention: The Scheduler has changed! To reproduce formerly generated membranes, use the old versions:
    • Distributor version 1.1 (now version 1.2)
    • Random Placing version 1.02 (now version 1.1)
  • strange limitation to a maximum of 9999 molecules for the PDB export removed
  • Java 7 compatibility issue with the substance package solved
    JColorChooser works now also with Java 7
  • fixed Java Web Start and Download Issues (new provider, 16.07.2012)
version 2.2.1_1

GCC (German Conference on Chemoinformatics) 2011 Release (04.11.2011)

  • save screenshot function added
  • stereo autofocus function added (for Java3D Stereo compatible graphic cards)
  • Statistics background adjust to the actual theme (dark or bright)
  • new OPM/PPM Server information added to Help and support implemented
  • new OPM alignment information added to Help
  • case-sensitive problem with directory Cm2/cm2images/icons solved
  • Cm2_IconDepot problems catched
  • problem with SortByType setting in ReversePDBParser solved
  • Developer Tutorial completely corrected
  • MyMembraneAlgorithm corrected (Example class of the Developer Tutorial)
  • Help slightly extended
  • JavaDoc comments of MembranePackingAlgorithm updated
  • 2 old lipids removed from library
  • backward compatibility with icon folder of the old Cm2_1 project added
  • Source Code: removed outdated TODO remarks
  • Source Code: version numbers in CHANGES.txt (this file) corrected
  • compatibility to optional GMX-Plugin version 1.1 (beta) for Gromacs added
version 2.2.1_0

Xmas 2010 Webstart Release (16.12.2010) to Cm2.2.1 Webstart & Source Code Release (23.05.2011)

  • 3D Stereoscopy Support added
  • PDB Writer refactored and enhanced
  • PDBTM and OPM Update issues with Linux and Windows fixed, canceling process improved, Contents Section in Downloads window improved
  • Source code completely refactored
  • MembraneAlgorithm package renamed to MembranePackingAlgorithm package, referring to our publication
  • Documentation extended and improved, citation and topology information for CmME, OPM, PDBTM and PDB added
  • Grace export integrated into protocol window for drawing algorithm runtime graphs
  • New compatibility information added into the PDB Output Settings for different PDB viewers
  • Parallel Projection and Uniform Background options added to 3D Settings

Milestones of the Cm2 development

23.05.2011 Release of Cm2.2.1

The first major release with source code under GPL license

source code and webstart version freely accessible

introduced in the first major publication in ACS JCIM

10.11.2009 WebstartPreRelease at the GCC2010

The PreRelease of Cm2.2

webstart version freely accessible

introduced at the German Conference on Chemoinformatics 2009 in Goslar

01.04.2009 PreRelease

The PreRelease of Cm2.1 Revision

restricted webstart access

2008 Cm2.1rev

The revision of Cm2.1 including 3D visualizations

internal development version only

2007 Cm2.1

Build from scratch version of the MembraneEditor, still with 2D visualization only

internal development version only

2006 Cm2.0

The first simple proof-of-concept version of the 2nd CELLmicrocosmos project

internal development version only

 

Cm2 is not the 2nd version of the MembraneEditor! Cm1 is a completely different software project unreleased yet.