 |
|
|
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 (
| |
