gOpenMol version 2.0 (31.03.2001)
New features in version 2.0
- All the discovered bugs in version 1.4 and 1.4p have been corrected.
- Cut planes through the grid data can be defined from 3 coordinates (atoms)
or planes perpendicular to the x, y and z axis.
- Clip planes through the grid data can be defined from 3 coordinates (atoms)
or planes perpendicular to the x, y and z axis.
- Coordinate reader has been improved.
- Coordinate reader for Jaguar output files.
- Filter program to convert Jaguar grid data files into gOpenMol
plt files.
- 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
- All the discovered bugs in version 1.3 have been corrected.
- New input coordinate formats have been added:
- Coordinate input can be read from Amsterdam Density
Functional (ADF) output log files.
- Coordinates from a GROMACS gro coordinate file.
- 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.
- New trajectory file format added:
- The GROMACS trn/trr/xtc trajectory file types.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- It's now possible to export the molecule(s) in their current
orientation and possition.
- 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
- All the discovered bugs in version 1.2 have been corrected.
- Tcl and Tk versions 8.2 are now in use.
- Coordinates can be exported as VRML models. So far only of the molecules.
Cutplanes, isosurfaces and orbitals will be implemented later.
- More line commands have got a graphical interface.
- Improved facility to run/edit Tcl scripts.
- Stereo pair display.
- Possibility to add atom symbols to the display.
- Possibility to edit light position and properties.
- Filter program to convert a grid file from the GRID program
into the format used by gOpenMol.
- Filter program to convert an AutoDock electrostatic grid file
into the format used by gOpenMol.
- A tutorial written by Scott Anderson.
- Commands that originally was written in C has been rewritten in Tcl
to enable flexible extensions and correction.
- 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
- 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.
- It's now possible to put gOpenMol in a full screen mode to support
the OpenGL PC-display cards.
- Atom partial charges can be imported from GaussianXX calculations
(log files).
- Time series can be exported to disk through the graphical GUI.
- It is possible to choose which structure is superimposed on which
structure.
- Possibility to edit the light properties.
- Possibility to use 9 different light positions. Please look at the
Edit Light properties.
- Possibility to display frame number while displaying a trajectory
frame.
- Improved tools to analyze AutoDock results (trajectories).
- 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.
- Facility to export the polygon coordinates, values and
normals from an isocontour display.
- Facility to display own polygon data.
- Ken Wilson at QTP Florida (http://www.qtp.ufl.edu/Aces2/) has prepared
a filter for the display of ACES II properties using gOpenMol.
- 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.
- 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)