Read e-book online Molecular Graphics on the IBM PC Microcomputer PDF

By James Henkel (Auth.)

ISBN-10: 0123408202

ISBN-13: 9780123408204

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Thus, these unwritten hydrogens can be termed implied hydrogens. The presence of these hydrogens in the structure often clutters the display and does not add any significant understanding to the problem. At other times, the presence of all or at least some of the hydrogens in a molecule is useful. If the structure of interest has been generated from X-ray coordinates or other coordinates from the literature, going back to add the hydrogen atoms is straightforward. However, if the structure has been generated by less traditional means (such as using the Space Tablet), then adding hydrogens can be quite difficult without reentering the entire structure.

Entry of numbers at this point is facilitated by the use of the keypad to the right of the keyboard. PCMODEL automatically activates the keypad by activating the NUM LOCK key from within the program. It also restores the cursor function at the end of the data entry session. Follow each coordinate entry by pressing ENTER. Until you press the ENTER key, you can correct a mistake by backspacing over the number, then retyping it. You can also erase the current entry by pressing the Esc key. After you have pressed the ENTER key for a given coordinate, you can not go back to correct a mistake until all the data have been entered.

When this has been accomplished, the structure is redrawn on the display screen and the program returns to command level. Note that atoms that were connected only to the deleted atom, such as hydrogens attached to a deleted carbon atom, will still be present on the screen but will not be showing. They can, however, still be located with the NUMBER command. Also, the numbers of the atoms that were higher than the deleted atom will have been changed to reflect the deletion. Be sure to check for any changes in the atom numbers before you delete a second atom, especially if it has a number that was higher than the first deleted atom.

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Molecular Graphics on the IBM PC Microcomputer by James Henkel (Auth.)


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