Working with molecular fragments


            Chemcraft allows one to construct molecules from standard groups of atoms (fragments). To add a new fragment to the displayed structure, select "Edit/Add fragment" menu item, then choose the required fragment from the list and then left-click on the main molecule's image. If you click on an atom in the molecule, the new fragment will appear near this atom, connected to it with a bond. If the clicked atom is a hydrogen or a dummy atom bonded with some other atom, the new fragment will appear bonded with that other atom, replacing the clicked atom. Similar actions are done when one adds individual atoms.

            One can add any group of atoms in displayed structure to the set of fragments. To do this, select the atoms which form a fragment and choose "Edit/Add selected fragment to database", then chose a directory and the fragment's name and press "Ok". If the fragment is a radical, the atom bonded with the outer molecule must be selected firstly. To delete the fragment from the set, or change its directory, choose "Tools/Supporting/Edit fragments database".

            Pressing Ctrl+C copies the fragment of selected atoms into the clipboard (in text format), pressing Ctrl+V adds the fragment from clipboard to current molecule. The rules of atoms selection are the same as for using "Add fragment" and "Add selected fragment to database" menu items.

            Here is an example of building acetone molecule:

 - Clear the displayed structure (choose "File/Clear" menu item).

 - Choose "Edit/Add fragment", then select -CH3 (subitem in the "-R" directory) and then click on the main molecule's image;

 - Select -CO- fragment (subitem in the "-R-" directory);

 - Click on the transparent dummy atom on the molecule's image;

 - Select -CH3 fragment;

 - Click on the transparent dummy atom on the molecule's image;

 - Press "Close";

 - The molecule is built, but the dihedral angles along the C-C bonds may correspond to wrong conformation. To change the conformation, select O,C,C,H atoms in the molecule, which form dihedral angles, and change their values in the textbox at the bottom of the window, then press the Set button. Another way is to switch into "Drag fragments" mode ( button, then ), then click on a C atom and press Num4/Num6 to rotate corresponding fragment (not releasing the left mouse button).