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Search for hydroquinone polymorphs.
Algorithm:
1. Open the window of the program IsoCryst again and draw a hydroquinone molecule. Select it.
2. Perform Select/Save Selection command and choose the file type Graph files (*.gph). Type the name hydroquinone and save the data. IMPORTANT! By default the *.gph files are stored in the GPH directory that can be assigned in System/TOPOS Parameters window (see also Appendix 9).
3. Close the IsoCryst window.
4. Choose Filters/Topology/Subgraph, press Load button and load hydroquinone.gph file.
Press View button to look at the molecule. Close the IsoCryst window.
5. Press Ok button. Four hydroquinone polymorphs out of 11 C6H6O2 compounds will be found.
6. Go to the second polymorphs in the list, open an IsoCryst window and perform Select/Load Tint File command. Choose Graph files (*.gph) and load hydroquinone.gph file. A Tint file data window will be open. There are three independent hydroquinone molecules in the structure. Perform Growth command in the IsoCryst window until all three records become bold.
Select all the three records (using Ctrl+Click or Shift+Click), set Options: Hide all atoms and click on Apply button.
The three molecules will be selected (in yellow) in the IsoCryst window.
Close Tint file data and IsoCryst windows.
Notes: Options: Hide none – in the figure all molecules will be kept and 3 among them will be selected by yellow. Options: Hide all atoms – in the IsoCryst window only 3 molecules will be presented, to be selected by yellow.
7. Select all four records in the database window and copy them into a new database Quinol.
Exercise: search for an arbitrary fragment in your own structures.
Algorithm:
1. Open the window of the program IsoCryst again and draw a hydroquinone molecule. Select it.
2. Perform Select/Save Selection command and choose the file type Graph files (*.gph). Type the name hydroquinone and save the data. IMPORTANT! By default the *.gph files are stored in the GPH directory that can be assigned in System/TOPOS Parameters window (see also Appendix 9).
3. Close the IsoCryst window.
4. Choose Filters/Topology/Subgraph, press Load button and load hydroquinone.gph file.
Press View button to look at the molecule. Close the IsoCryst window.
5. Press Ok button. Four hydroquinone polymorphs out of 11 C6H6O2 compounds will be found.
6. Go to the second polymorphs in the list, open an IsoCryst window and perform Select/Load Tint File command. Choose Graph files (*.gph) and load hydroquinone.gph file. A Tint file data window will be open. There are three independent hydroquinone molecules in the structure. Perform Growth command in the IsoCryst window until all three records become bold.
Select all the three records (using Ctrl+Click or Shift+Click), set Options: Hide all atoms and click on Apply button.
The three molecules will be selected (in yellow) in the IsoCryst window.
Close Tint file data and IsoCryst windows.
Notes: Options: Hide none – in the figure all molecules will be kept and 3 among them will be selected by yellow. Options: Hide all atoms – in the IsoCryst window only 3 molecules will be presented, to be selected by yellow.
7. Select all four records in the database window and copy them into a new database Quinol.
Exercise: search for an arbitrary fragment in your own structures.
