gOpenMol version 2.3 (23.9.2003)

This version is a rewrite of a significant part of the kernel code to improve the graphics display speed and to enable the plugin feature. The structure of the program is now more logical and it's easier to add new tools into the program. The Linux make has been totally rewritten and already this should ease the process to install gOpenMol on other platforms.

The main platforms are still Win32 and Linux. Due to lack of resources we will not promise versions for other platforms, at least not any time soon.

gOpenMol version 2.2 (23.9.2002)

This version has gone through a quite comprehensive updating and therefore this list of new features is rather long. Hopefully you will find time to read it through.

Atom connectivity

• Citeria to determine atom connectivity can be customised. A bond between two atoms is created if the distance between the atoms is equal to sum of covar radius of the atoms (a small delta is accepted). The covar radius can be changed temporarily from View - Periodic table and permanently by editing the file data/element.data.

Atom labels

• New atom label type has been added. In addition to the previeously available labels atom name and full name it is now possible to display residue name and number. This feature is specially for protein structure analysing.
  
  Go to View - Atom label(s)... to test this.
  
  

Atom picking

• Atom picking has got quite a few new features. The atom picking mode can be turned on and off by marking the respective radio button. When the mode is on, just click on an atom in order to pick it. Atom picking can also be used by pressing down Ctrl and clicking with left mouse button (LMB) on top of the atom one wants to select. This feature can be utilised in the following way when you want to modify an atom or an group of atoms.
  
  
  • A single atom can be picked and it can be dragged and dropped to a text widget by picking the atom pressing down LMB and dragging the cursor to the text widget.
  • If several atoms are picked, they can all be dragged and dropped to a text widget by pressing down LMB on an empty space in the 3D window and dragging the cursor to the text widget.
  
  
• The atoms can be unpicked by holding down Ctrl-button and clicking at the same time with LMB over the picked atom, if the "Pick Atoms" radio button is turned off. If "Pick atoms" is turned on, just click with LMB over the picked atom to unpick it. You can also unpick all atoms by clicking the Unpick all-button.
  
  

Atom selection

• Selected atoms are marked using cubes to separate them from picked atoms, which are marked with spheres. Atoms can be unselected by clicking Unselect all -button in "Select atoms"-window.
  
  Go to Edit - Select... to test this
  
  

Atom tree

• A new level has added to the Atom tree. This applies only to protein structures, where now the residues will be listed first and atoms in the residues are listed under every residue.
  
  
• Structure and segment names, residue names and numbers and atom names can be modified by clicking once on the item and then clicking it again.
  
  NB: This does not mean double-clicking! There has to be a short delay between the two clickings.
  
  A box will appear around the selected item and a cursor will start to blink. After the editing has been done, press enter and the item is now modified. If the modification had an effect on atom tree hierarchy, the appropriate tree items will not be created automatically. Just press the Update-button to update the "Atom tree".
  
  
• The element type of the atom, atom coordinates, colour, van der Waals radius and charge can be modified in the same way as the atom names. Colour can be changed either by giving a RGB-value for the wanted colour or by typing the name of the colour instead of the numerical values. If you have changed any of the parameters in the "Content"-part of the "Atom Tree"-window, the updating is done automatically and you do not have to click the Update-button.
  
  Go to View - Atom tree... to test this.
  
  

Display lists

• The program supports the use of the OpenGL display lists for all complex objects. The use of display lists reduces the need to repeatedly call the same low level graphics calls and can therefore make graphics display updating faster. This is especially true when running the program over a slow X11 connection and there is an OpenGL extension in X server.
  
  Go to Edit - Display list properties... to turn them on.
  
  

Extension support

• Support for extensions (Dynamic Linked Libraries (DLL) in Windows and Shareable Object (SO) in UNIX) in improved.
  
  

Hydrogen bonds

• Hydrogen bonds can be recalculated for trajectory frames.
  Go to Trajectory - Main... In the "Trajectory Control"-window there are "on" and "off" radio buttons for "Hbond recalculation" where this function can be turned on and off.
  
  
• Hydrogen bonds are searched using a search subset. So if one wants to show only some of hydrogen bonds it is possible to define small search subsets around those atoms. In some circumtances this can significantly reduce the search complexity.
  
  Go to Calculate - Hydrogen bonds...
  
  
• The criteria how to calculate hydrogen bonds can be changed.
  
  Go to Calculate - Hydrogen bonds and click Change criteria
  
  

Import and export of the coordinate files

• gOpenMol can now identify most of the coordinate file types supported by the program based on the file extensions. In the "Import coordinates"-window this autodetection property is on by default. File format can still be selected manually but it should not be necessary unless the file formats, which do not have standard file extension, are being used. In the "Export coordinates"-window the autodetection property is off by default but can be turned on if needed.
  
  
• Ability to import from and export to atom coordinates of Chemical Markup Language (CML) file is added.
  
  
• The start-up routine uses the same autodetection property when it searches input filter for files given in command line. The coordinate file filter search routine is reimplemented so that support for a new file format can be added without recompailing the program source code.
  
  

Plumbers

• In former versions only helices and sheets were listed in plumber secondary structure window. Now the program also finds loop regions. In addition the whole protein chain is listed as trace.
  
  Go to Plot - Plumber... and click the Click for information -button next to the text "Secondary structure:" to view this.
  
  
• Two new plumber types are added: strand and trace. Trace will create a line and strand a ribbon through all selected atoms.
  
  
• By using fast draw option in Edit - Display properties the plumbers are drawn as lines during rotation so they do not disappear completely.
  
  Go to Edit - Display properties... and mark the Redispaly type "Fast" radio button.
  
  
• Plumbers can be glued to atoms. The points of glued plumbers are relative atom positions and will therefore move along atoms. This might be useful feature then using trajectories. The more important advantage, though, is the extra residue information in plumber list window.
  
  Go to Plot - Plumber... to test this feature. In the "Plumber"- window there is a box next to text "Glue to atoms". If this is marked, the gluing is on and if not, the gluing is off.
  
  
• Plumbers can now be listed, modified and deleted in the "Plumber list"-window. Listing shows the plumber type, the name of the structure containing the plumber, the segment and the residue names and the number of the first and the last residue of the plumber. Segment and residue information is available only if the plumber is glued to atoms. The colour of the plumber can be changed and the plumber can be unglued from atoms.
  
  Go to Plot - Plumber... and click the List plumber(s)- button to view and edit the Plumber list.
  
  

New command lines

• Four new command lines have been added. To view their properties, type
  
  help edit hbsubset,
  help find,
  help show plumber or
  help plumber
  in the command line interpreter.