Chapter 5. Drawing Tools
The palette of drawing tools appears at the left-hand side of the drawing window when PCMODEL program is started. The palette can be moved anywhere on the screen by dragging on the "Tools" title. The window can be closed by clicking on the CANCEL button at the very bottom, and recalled by selecting DRAW from the EDIT menu.
This option allows certain atoms to be selected for action by future commands. As many atoms as desired can be selected. To clear all selected atoms, click again on the SELATM button
This option allows bonds to be selected for action by future commands. As many bonds as desired can be selected. To clear all selected bonds, click again on the SELBND button
This command enables the drawing mode. To create a new structure, select DRAW then move the cursor to the desired location and click the left mouse button. If the cursor is then moved to a new location and the left mouse button is clicked again, a line will be drawn, indicating a bond between the previous atom and the new one just placed. If the cursor is moved to a new location and the left button is clicked again, a third atom will be created and bonded to the second atom. Note that all atoms are added in the plane of the screen.
To close a ring, place the cursor on an existing atom and click the button. The cursor must be within about 1/4 inch of an atom to draw a bond to that atom instead of creating a new one. A small box will appear around the atom when the cursor is close enough. To start drawing from an existing atom without adding a new bond to that atom, click on DRAW again, place the cursor on the old atom, click and continue drawing as before. New atoms will be added in the same plane as the last atom picked. To start drawing from a new location, click on the DRAW button again then move to the new location and click the mouse. A small dot will appear indicating a new atom.
Clicking on DRAW, then selecting first one end of the double bond, then selecting the other end may create double and triple bonds. Conventional double lines will be used when the structure is redrawn. Alternatively, the ADD_B option can be used (see below). If there are many multiple bonds, this is the easier method to use.
This option allows for rapid building of 3-D structures. After selecting BUILD, click on any hydrogen and it will be replaced with a methyl group. This option allows PCMODEL to provide the 3-D information required to build the structure, as opposed to the DRAW option, where all atoms are added in the plane of the atom to which they are connected. (Or, in the plane of the screen, in the case of unattached atoms.) The structure may be rotated and viewed with tubular bonds to get a better 3-D view of the molecule. The Stick Figure view is best for selecting atoms.
This option redraws the screen, and updates the structure with any changes since it was last drawn. It clears any Query information.
This command will automatically add or delete hydrogens and lone pairs. The structure will be redrawn with the appropriate structure. Hydrogens and lone pairs attached directly to metals will not be removed. Hydrogens attached to oxygen and nitrogen are not removed to preserve the orientation of hydrogen bonds.
Note that removal of hydrogens followed by re-addition will not necessarily return you to the original structure. Hydrogens are added according to a geometric prescription. To remove hydrogens for viewing or comparison purposes only, use the H/OO command (see below).
This command increments the value of the selected bond by one (single to double to triple). After selecting ADD_B, click in the center of the bond to be incremented. An X will appear over the bond when you are close enough. The structure will be redrawn with the conventional double or triple line representation.
This command pushes selected atoms behind the plane of the screen, by approximately 0.33 Å. Each time an atom is clicked on it will be pushed in an addition increment.
This command pulls selected atoms out of the plane of the screen, by approximately 0.33 Å. Each time an atom is clicked on it will be pulled out an addition increment.
This command DELetes an atom or bond. After selecting DEL, click once on each atom or bond to be deleted and the structure will be redrawn with the atom or bond deleted If an atom is deleted, all bonds to that atom are deleted, as well as any attached atoms. Thus, you only need to click on the carbon to delete an entire methyl group. It is important to do an H/AD command before writing a file if any atoms or bonds were deleted. This ensures that any "holes" created but not removed from the arrays will be removed during this process and that the heavy atoms will be in the proper sequence.
This command moves an atom into a new position. After selecting MOVE click on the atom to be moved, then click in the new position. The structure is redrawn the atom will be moved. Multiple MOVEs may be done at one time, until another option is chosen.
This command rotates the central bond of the four selected atoms. Use SELATM to first select the four atoms. The selected atoms will be marked by small gray dots.
This command is used to measure atom positions and charges, bond lengths, angles and dihedrals. To determine the position and charge of an atom select QUERY click on an atom and then a blank space on the screen. To measure a distance, select QUERY, click on the two atoms whose distance is to be measured, then click on a blank area of the screen. The distance between the two atoms will be displayed on the screen at the location of the last click. To measure an angle, click on the three atoms forming the angle of interest, then a blank area of the screen. The numerical value of the angle will be displayed. Similarly, to measure a torsion angle click on the 4 atoms of the torsion then a blank area. If you select two vicinal hydrogens or if you select four atoms of a dihedral and the first and last atoms are hydrogens the PMR coupling constant will be calculated. The PMR coupling constants are corrected for electronegativity according to the method of Haasnoot, DeLeeuw and Altona, Tetrahedron 1980, 36, 2783.
Any number and combination of distances, angles and torsion angles may be measured, until another option is chosen. The queries can be printed and will remain on the screen during minimization and dynamics calculations so that changes in the structure can be monitored. To clear the values from the screen, click on UPDATE twice.
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This command calls up a window containing a list of atom types. An atom may be changed to a different type by selecting the new type from the Periodic Table window, then clicking on the atom to be changed. Multiple atoms may be changed to the same type without re-selecting the type. A complete listing of atom types is given in the MMX Force Field chapter. Clicking on CANCEL closes this window.
5.14 Metals
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This command calls up a window containing a list of metal atom types. An atom may be changed to a particular metal by selecting the appropriate metal from the list, then clicking on the atom to be changed. The electron count (saturated, unsaturated, high spin, low spin or square planar), charge and coordination of a metal to a pi system are set with the Metal Coord menu item in the Mark Menu. Clicking on CANCEL closes this window.
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This command calls up a window containing a list of ring templates. A complete listing of the rings is given in Appendix B. Selecting a ring from the list causes that structure to be placed in the structure window as a new substructure. Clicking on CANCEL closes this window.
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This command opens a dialog box containing 24 standard amino acid residues. Selecting one of the amino acids causes that structure to be drawn in the structure window. If the CONNECT box is selected, the secondary structure of the connection (alpha helix, beta sheet, beta turn type I or beta turn type II) must be specified prior to selecting the amino acid sequence. Clicking on CANCEL dismisses this window. A complete list of all the amino acids is given in Appendix B.
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This command opens a dialog box containing 25 standard sugar residues. Selecting one of the names causes the corresponding structure to be drawn in the structure window. If the CONNECT box is checked, the structure of the connection (alpha or beta) must be specified prior to selecting the sequence. Clicking on CANCEL dismisses this window. A complete listing of all the sugars is given in Appendix B.
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This command opens a dialog box containing 5 nucleosides. Selecting one of the names causes the corresponding structure to be drawn in the structure window. The default is to draw DNA, but clicking on the RNA button instead may draw RNA. If the CONNECT box is checked then a letter symbol representing the Nucleoside chosen will be written in the edit box. When all the nucleosides are entered selecting Build will generate a single strand of DNA or RNA. Selecting Build Double will build a double strand. Clicking on CANCEL dismisses this window. A complete listing of all the nucleosides is given in Appendix B.
5.18 Organo Metallics Templates
This command calls up a window containing a list of organometallic templates. These are structures that have been built and saved in a file. Selecting a structure from the list causes that structure to be placed in the structure window as a new substructure, which can then serve as the starting point for building new structures. Clicking on CANCEL closes this window.
5.20 Transition State Templates
This command calls up a window
containing a list of transition state structures. These are structures that
have been built and saved in a file. Selecting a structure from the list causes
that structure to be placed in the structure window as a new substructure,
which can then serve as the starting point for building new structures Clicking
on CANCEL closes this window.