gOpenMol version 2.0 (31.03.2001)

New features in version 2.0

  1. All the discovered bugs in version 1.4 and 1.4p have been corrected.
  2. Cut planes through the grid data can be defined from 3 coordinates (atoms) or planes perpendicular to the x, y and z axis.
  3. Clip planes through the grid data can be defined from 3 coordinates (atoms) or planes perpendicular to the x, y and z axis.
  4. Coordinate reader has been improved.
  5. Coordinate reader for Jaguar output files.
  6. Filter program to convert Jaguar grid data files into gOpenMol plt files.
  7. Filter program to convert "cube" data in PC Gamess PUNCH files into gOpenMol plt files.

gOpenMol version 1.4 (01.06.2000)

New features in version 1.4

  1. All the discovered bugs in version 1.3 have been corrected.
  2. New input coordinate formats have been added:
    1. Coordinate input can be read from Amsterdam Density Functional (ADF) output log files.
    2. Coordinates from a GROMACS gro coordinate file.
  3. The trajectory readers have been changed to enable the reading of binary trajectories indipendent of hardware. In principle it should now be able to read trajectories without the need to format/unformat them when moving from one hardware platform to an other.
  4. New trajectory file format added:
    1. The GROMACS trn/trr/xtc trajectory file types.
  5. Binary plt plot files can be moved between hardware platforms without the need to reformat them. The gOpenMol plt file reader can now do the byte swap on the fly.
  6. It is now possible to select atoms by clicking on them and dragging them into an input widget. This makes it easier to pick atoms into input widgets.
  7. All molecular systems read into gOpenMol has its own viewing matrix enabling the rotation/translation of individual molecules. The two modes are defined as global and local transformations. In the global mode all the molecular systems rotate/translate to a common center while in the local mode the translation/rotation will be according to an individual coordinate center.
  8. To enable quick rotation, translation and picking it is possible to enable the translation mode by pressing the Shift key before one presses the left mouse. As long as the Shift key is and the left mouse button are pressed the structure will translate when the mouse is moved. Be careful to understand that if the Shift key will be released before the left mouse button the Translate state will be left on. In the other case Translate mode will return to Rotate mode.
  9. By pressing the Ctrl key first and keeping it pressed it is possible to pick or mark atoms in the graphics screen by pressing the left mouse button. The selected atom(s) can then be dragged to an input widget. If one releases the Ctrl key before releasing the left mouse button gOpenMol will stay in the picking mode.
  10. Pressing the Alt key and the left mouse button and moving the mouse in the x-axis direction rotates the molecule around the z-axis. This is the same as using the middle mouse on a three button mouse.
  11. In the Edit menu there is now an Atom Browser that opens as a tree. The atoms in the tree can be clicked. The clicked atom will show up in the graphics screen as being selected. It also works the opposite way. Clicking an atom in the graphics window will highlight the clicked atom in the atom tree. The atom tree also shows a lot of atom information. In the future there will be a feature to edit the parameters.
  12. All input file names can be given as a http link and thus be read from a Web server. If you know that there is a file named myfile.crd on a server named my.server.org the input file name can be given as http://my.server.org/myfile.crd.
  13. Filter program (gamess2plt) to read the "CUBE" information from the PC Gamess v. 6.0 PUNCH file and convert it into a plt file. The v. 6.0 of PC Gamess can now produce "CUBE" file information, like the information GaussianXX programs produce, into the PUNCH file.
  14. It's now possible to export the molecule(s) in their current orientation and possition.
  15. It's now possible to merge two or more structures into one with the molecules in their current orientation and positions.

gOpenMol version 1.3 (September 1999)

New features in version 1.3

  1. All the discovered bugs in version 1.2 have been corrected.
  2. Tcl and Tk versions 8.2 are now in use.
  3. Coordinates can be exported as VRML models. So far only of the molecules. Cutplanes, isosurfaces and orbitals will be implemented later.
  4. More line commands have got a graphical interface.
  5. Improved facility to run/edit Tcl scripts.
  6. Stereo pair display.
  7. Possibility to add atom symbols to the display.
  8. Possibility to edit light position and properties.
  9. Filter program to convert a grid file from the GRID program into the format used by gOpenMol.
  10. Filter program to convert an AutoDock electrostatic grid file into the format used by gOpenMol.
  11. A tutorial written by Scott Anderson.
  12. Commands that originally was written in C has been rewritten in Tcl to enable flexible extensions and correction.
  13. A crude manual is available in the doc directory. For new versions please check the Windows Word file: http://laaksonen.csc.fi/gopenmol/docs/gopenmol-manual.doc

New features in version 1.2

  1. Programming of the 12 function keys. The user can now program frequently used commands behind the 12 function keys. Please look at the beginning of file data/gopenmol_guirc.tcl file.
  2. It's now possible to put gOpenMol in a full screen mode to support the OpenGL PC-display cards.
  3. Atom partial charges can be imported from GaussianXX calculations (log files).
  4. Time series can be exported to disk through the graphical GUI.
  5. It is possible to choose which structure is superimposed on which structure.
  6. Possibility to edit the light properties.
  7. Possibility to use 9 different light positions. Please look at the Edit Light properties.
  8. Possibility to display frame number while displaying a trajectory frame.
  9. Improved tools to analyze AutoDock results (trajectories).
  10. Possibility to display both the structure and a ldp simultaneously. Clicking on the ldp window is displayed in the structure window as an array connecting the two atoms defining the distance.
  11. Facility to export the polygon coordinates, values and normals from an isocontour display.
  12. Facility to display own polygon data.
  13. Ken Wilson at QTP Florida (http://www.qtp.ufl.edu/Aces2/) has prepared a filter for the display of ACES II properties using gOpenMol.
  14. A filter routine written by Jonas Juselius, Department of Chemistry, University of Helsinki, to convert TURBOMOLE moloch grids into a format recongized by gOpenMol. Please look into the utility/turbotools directory.
  15. An improved version (g94cub2pl.c) of the gcube2plt.c by Doug Moffatt, Technical Officer National Research Council of Canada. Please look into the utility/ directory

Leif Laaksonen (2000)