Impressions ChemKrist-
Workshop 2013



Getting started with GTECS

This section is still growing - Come back later for more...

Installing and execution

For installation download the correct version and extract the folder to the desired location on your system (please avoid blanks in the path). On Windows start the "gtecs3dgui.exe", for Linux execute the "start.sh" script.

Open a cif-file

Opening a cif-file in GTECS can be either done by drag and drop onto the GUI-window or by browsing via the menu to the desired file. You can also type in the path of your file in the command line. Please avoid blanks in your path.

start path-to-your-file/yourfile.cif

If the structure is loaded succesfully the scene-window will pop up displaying your structure. Furthermore some properties (number of components, directions of infinite fragments etc.) are shown in the log-frame of the gui tab. In the following example we will use the build in structure which will start if you don't load a valid cif file.

Navigation

Navigation through the scene is done by mouse. Holding the left button lets you rotate the scen, holding the right button is for panning. Zooming is done by holding the middle button on your mouse.

Selection

Atoms can be selected by clicking on them. For multiple selection the "b"-button on the keyboard has to be pressed. You can also find a shortest path between two selected atoms by holding the "v"-key or expand your selection by pressing "e". All selected atoms are listed the "Sceneinfo" tab.

Simplification

Selected atoms can be reduced to one vertex if they are connected to eachother by clicking on "Combine" in the "Sceneinfo"-tab. But this is not the powerful simplification feature of GTECS:
The "Gui"-tab provides useful automated algorithms. E.g the "Reduce Vertices" function. For the default structure you can see how clicking on "Degree 1" removes all "dead end" in the network. Executing the algorithm "Degree 2" twice leads to the very simple underlying net, whose topology can now be calculated.
Another automated simplification function is the ring contraction. Select the desired ring size in the "Gui"-tab and press "Contract Rings". Atoms building a ring of the specific size are reduced to one node in the center, preserving all connections to other atoms.

Topology Calculation

If your structure is simplified (e.g. start - Degree 1 - Degree 2 - Degree 2) you can calculate the topology of the net. Here you have to choose if you want to search for cycles or rings (c.f Conventions for topological indices). Please note that selection rings can sometimes lead to very long computing times.

Example

Follow this example on your own PC to get a better experience of the included functions.

You should get the following result for Ag- and Al-centers:

cycle: 4(1) 4(1) 4(1) 4(1) 6(2) 6(2)
ring:  4(1) 4(1) 4(1) 4(1) * *
Now you can use the sceneinfo tab for creating a suitable picture:
Select one atom in the scene and press "e" on your keyboard to expand the selection to the entire net. Click on "choose color" and select the desired hue. The alpha-channel is for creation of transparency. Clicking on "set color" will colorize the selected atoms. Now you can select the other net and paint it with a different color.