Book 4. HIDE & SHOW-

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All these buttons are toggle switches. Their functions should be self evident. They switch to prompt whether to 'hide' or 'show' an attribute automatically with the following exceptions: Fields, which will be discussed later, come in three 'flavours' - green (-ve), orange (+ve) and yellow ('sticky'). The toggles for these are coloured but their state must be judged from the display. There is only one page to Book 4 (no *)

It is important to realise that these switches DO NOT REMOVE the attributes- they merely HIDE them. Removal of attributes is done in Book 5....

Book 5. ADD & REMOVE -

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'Removal' in Book 5 means REMOVAL. You may feel that removal followed by addition is the same thing as 'hide'. However, if you have minimised a structure or a molecule that has been constructed from X-ray or other experimental sources, its hydrogen bond lengths will be important. Addition of hydrogens after removal does not re-instate the old hydrogens but constructs new hydrogen positions based on the computer's idea of their length and geometry. Adding new hydrogens, XEDs and bonds will require reminimisation!

ADD & REMOVE Hydrogens:

Clicking here removes any hydrogens if they are present. If no hydrogens are present, this button will create new hydrogens.


XEDs (eXtended Electron Distributions) will be covered in Appendix 4. The action of this button is the same as the 'Add/remove H' button. XEDs will not be added automatically if partial charges are absent. Removal of XEDs sets partial charges to zero.


Molecular Fields will be covered later. They can be removed using this button. Partial charges and XEDs are left intact.


This is a special button. Fields can be constructed on a molecule (see BOOK 6) which indicate the way the molecule might react to another molecule. It will become apparent that these fields can be used as 'templates' to find similarity and dissimilarity amongst molecules. The use of a field as a template requires that it has no structure associated with it. This button removes all structure from a molecule with fields, leaving just the field itself linked to a dummy centroid. This constitutes a 'template'.


Dummy atoms are created for centroids, normals, centres and field foci. They can be removed en bloc with this button. Dummies will not go through the minimiser and cannot be used in molecules that are to undergo conformational hunting, dynamics, field creation or field comparison procedures.


Part of a molecule can be removed with this button. After clicking on the button, you are asked to pick 2 atoms which represent the bond where fission will take place. All structure linked to the 1st atom you pick, will be retained. Structure beyond & including the 2nd picked atom will be lost. It will be obvious that picking two atoms which are in a ring, is not allowed. The computer will prompt you in this case. It will also prompt your if it thinks that the atoms you have picked will result in the loss of the whole structure. This is done with the next button:


After clicking this button, it is necessary to define which molecule you want to remove. Only 1 atom belonging to the fated molecule needs to be picked and the whole molecule will vanish. If there is only one molecule on screen and you try to remove it, the system will return the last temporary structure that was dumped (quietly) as a safety measure.


After clicking on this button, pick two atoms. If there is a bond between them, it will be removed. If not, a bond will be formed between them.


Once this button is activated, you may pick as many atoms as you wish to remove. Removal of those atoms will only occur when the yellow instruction at the left hand lower display screen is clicked. All the bonds associated with the lost atoms are also removed.

You will note that there is a red star at the top left hand corner of both books 5 and 6. These turn extra pages which are associated with multiple file (multi-file) reading. See later for details.

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