In the Bond tab, all bonds in which centroids are involved should be blanked out, and for the bonds between atoms choose an eye-catching colour:ġ9. the polyhedra have to be rendered as “Rendered solid”, all atoms as “Stick bonds”.ġ8. In the Atom tab all new centroids (Zz and so on), i.e. Now, only some slight setting modifications have to be done – choose “Model – Model Inspector…”. A new Centroid is created, here coloured in blue:ġ7. Then select all atoms of one kind of polyhedron and choose “Selection – Make Polyhedron…”. Expand the view so that all polyhedra are clearly visible, remove additional bonds by adjusting the bond length. Run CrystalMaker and Import the file net-a.cif. Import the Systre file into a new database in ToposPro. Name it for instance “net-a_systre_out.cgd” to distinguish between the input and output file.ġ3. After a few seconds Systre has finished and you can save the net with the highest possible symmetry by choosing “Save as…” and by specifying the format as “”Embedded nets type (*.cgd)”. Systre tries to relax the nodes so that a) the average bond length is 1.000 Å and b) that the symmetry of the net is maximized.ġ2. Export the file from ToposPro into the Systre format (*.cgd).ġ1. Now, try to maximize the symmetry with the help of Systre (which is part of the package Gavrog ). Turn the additional bonds into “No bond”. Remove the additional bonds by modifying the corresponding adjacency matrix. There are some additional bonds and it is probably not the most symmetrical representation. It looks quite okey, but two things are not correct. In the case of the reo net the result will look like this:ĩ. Remove all 2-c boron atoms: Choose “Compound – Auto Determine – Simplify Adjacency Matrix” – remove all 0-, 1- and 2-coordinated vertices. This entry has to be modified a little bit.Ĩ. You will get a new database “net-a_c” containing one entry. Run ADS in the standard simplification mode (Save Simplified Net/Standard), but with the option “Contract Atom” under the tab “Topology” checked.ħ. Repeat this procedure, choose “Compound – Auto Determine – Bond Midpoints” again.Ħ. Go to “Compound – Auto Determine – Bond Midpoints”. Now we can create the augmented variant within ToposPro.ĥ. Copy the entry of choice (here reo ) from the “idealnets.cmp” into the newly created database. Even if the coordinates of the augmented version of a net is not in your database “idealnets.cmp”, it is very likely that the coordinates of the basic net are available in the ToposPro database “idealnets.cmp”.ģ. But, if the net from which you want to make a nice-looking figure is present, proceed with step # 15.Ģ. 3000 nets, within ToposPro and look-up, if you can find the desired net. Open this database, which contains approx. There are two possible sources:Ī) RCSR (please checkmark the “including augmented version” option) – for reo the search is unsuccessfullī) ToposPro is delivered with a database called “idealnets.cmp” (search with your File Explorer to find this file). the space group of the net and the fractional coordinates of the nodes. In general, you need the structural information of the net-a net, i.e. In this tutorial we want to make an image of the net reo-a.ġ. Although the gorgeous freeware VESTA has also some capabilities in that respect it is, unfortunately, not suitable. Two of the most frequently used (commercial) packages for this purpose are Diamond and CrystalMaker.
There is one requisite in order to be able to create and make great looking images of augmented nets: A software package that has the option to make and show customizable coordination polyhedra. Making beautiful pictures of beautiful nets in augmented version