Aromaticity
Aromaticity is perceived in 6-membered rings only (with C, N and P atoms); in the case of HyperChem files in 5-membered rings too. If the target molfile/program supports the use of aromatic atom and/or bond types, a message box appears and you may select: to use alternating single/double bonds in the aromatic rings, or aromatic atom and/or bond types.
The appropriate selection of correct atom/bond type (aromatic versus S/D) is important, and must be chosen according to the target program. Prefer the use aromatic types in the case of Alchemy, Sybyl, HyperChem, Insight, Moby, but in PCMODEL both are allowed, depending upon the method of geometry minimization (with/without pi-electron calculations) used. Generally, if MM-type calculations will be made with the molecule of the new file, choose the aromatic option, in the case of semiempirical quantum chemistry calculations you may use both ones. If you use S/D bonds ChemWindow, ISIS/Draw, ChemText, PLT will draw S/D bonds in the benzene rings, but on selecting aromatic bonds a circle will drawn by ChemWindow and dotted lines in the other programs.
Atom names or named (labelled) atoms
In some file formats the atom numbering is attached to the chemical atom symbols, like in some crystallographic files: C1, C2, H3, H4, S(12) etc. Atom symbols can be easily deduced from these. In another files atom names are not so straightforward, like in PDB (Protein Data Bank) files: CA, CB, CE1, HB1 etc. In this case atom names correspond to given places in the amino acid moieties. To decode these, most high-end programs use residue libraries of the names & structures.
Atom types:
Simple modelling and drawing programs use only natural atom types (C, H, N, O etc). Sometimes atom numbers are to be used instead (6, 1, 7, 8 etc), some programs use named atoms. More sophisticated programs use extended atom types, therefore for example instead of single C several other carbon atom types are used: sp3, sp2, sp, aromatic, transition etc. Dummy atoms and lone pairs may also be supported. Among the currently supported molfile formats Alchemy, SYBYL, PCMODEL, HyperChem, Macromodel, Insight and MOBY use extended atom types. During an upward transformation, Mol2Mol will calculate the necessary extended atom types, provided the molfile contains the hydrogen atoms, and the bond lengths and angles are correct. For definitions of the supported atom types of the different programs see the individual programs under supported molfiles.
Centering of the molecule:
Centering the original (world) or screen coordinates at the centroid of the molecule or at the cursor atom.
Dummy atoms
Dummy atoms are used in some programs in place of unsupported natural or extended atom types. In quantum chemical or force field calculations dummy atoms may be used to fix a required spatial orientation of the "normal" atoms. If the use of dummy atoms is supported, various symbols are used by the different programs: Du, Xx, -1 etc. Mol2Mol uses the appropriate symbol, if the target program allows the use of dummy atoms. In the case of Z-matrices you have to know the precise format of the target program to decide which symbol is to be used. For more details see Z-matrices.
Lone electron pairs
Some programs, which use extended atom types, may support lone pairs too. The support of lone pairs may vary within the program according to the type of the force field. They are designated by the symbol Lp or a special number. Mol2Mol takes into account the use of lone pairs. If a structure which is to be input contains lone electron pairs, the program may leave them, remove them automatically or ask whether you want to remove them or not, according to the settings in the Preferences window. You can remove them later using the Remove lone pairs option in the main Edit menu. In most circumstances it is better to remove them, however, this depends on the target programs.
Molecule file or molfile
An (usually) editable ASCII file which contains at least the natural atom types (C, H, N, O, etc) and the atom coordinates. Connectivity (bonds) and bond types (single, double, etc) are also usually included. It may include extended atom types. For technical and practical reasons, in the File input menu there are three options for inputting the files:Molfiles (marked by the letter M in the Molecule files window): all of the files described above, except:
Crystal files (C): Files usually containing fractional coordinates. They are created by programs used for X-ray structure elucidation or used by crystallographic data bases.
User's general file (U): These may contain Cartesian or internal (Z-matrix) coordinates and any kind of other numerical or textual information in a free format. A marker character must be manually inserted at the beginning of the coordinates.
Upward transformation
Modelling programs can be divided into two groups. In group 1 are those that use only "natural" i.e. C, H, N, O etc). In group 2 are programs which differentiate a large number of subtypes of the same atom (like C sp2, C aromatic etc). If the target program belongs to group 2 during the conversion, the atom and bond types must be calculated (upward conversion). The aromatic bonds are converted to alternating single and double bonds or to special aromatic types (if the target program will accept both, you will have to decide which one to use). "Query" bonds are translated into single bonds, if necessary.
LED indicators
Green light: the program is idle and is waiting your next command
Coordinate system indicators
When red, signals that the world or screen coordinate system has been changed.
Indicators
When highlighted, these status indicators mean that the current structure contains:| Cp | partial atomic charges; |
| Cf | formal atomic charges; |
| Ar | aromatic atoms; |
| Lp | lone-pairs; |
| Du | dummy atoms; |
| 3D/2D | three- or two-dimensional coordinates; |
| noH | no hydrogens; |
| noB | no bond type information; |
Indicators
When highlighted, these status indicators mean that the current structure contains:| Bat | the program operates in batch input/output mode (many-to-many, many-to-multiple); | ||||||
| Mul | the program operates in input/output multiple input/output mode (multiple-to-multiple); | ||||||
| Spl | the program operates in split input/output mode (multiple-to-many); | ||||||
| Bro | Browse input mode is active; | ||||||
| PDB | (green if active) "genuine" PDB file was inputted, or seems to be PDB-like from other source.
| Mo | (yellow number if >1) number of inputted models (usually from PDB files) or molecules;
| Ch | number of inputted chains;
| Re | number of inputted residues;
| |
Bond indicators
When highlighted, these indicators mean that the current structure contains:| 1 | single bonds |
| 2 | double bonds |
| 3 | triple bonds |
| am | amide bonds |
| ar | aromatic bonds |
| co | coordinative bonds |
| io | ionic bonds |
| w | weak bonds |
| du | dummy bonds |
| nc | no-connection bonds |
| un | unknown bonds |
| st | stereo bonds |
Graphics window
The graphics window can be switched on or off if a molfile was input successfully.
File info
The name, type, length and date of the current molfile is shown here. During input, some other information may also appear in this status area.
Text window
Program messages, information, calculated geometrical data, remarks included in the molfiles etc appear in this scrollable message area. The size of the text buffer can be changed in the Preferences.
Type of graphics
You may select the style of the graphical display as normal, stereo red-and-green or stereo cross-eyed. Note that in stereo modes not all of the other buttons are available. For cross-eyed mode, change the width of the graphics window to get an appropriate distance between the two pictures.
Zoom in/out
Zoom + and - buttons magnify or diminish the display of the whole molecule. This is also possible with the mouse (shift L-drag), when the cursor is in the graphics area.
Fix image size
The subsequent molecules will not be automatically fitted and sized. Can be useful in the browse mode when for example inspecting the different chains of a peptide.
Size of the atoms
These buttons make the atoms larger or smaller relative to the size of the structure. When the atom numbering is being displayed, the font size of the numbers are affected by these buttons.
Show hydrogens
Toggles the display of hydrogen atoms on and off.
Show axes
Toggles the display of the coordinate axes on and off.
Colour
Toggles between colour and black & white display mode of the structure. You may want to use the black & white mode, when copying the structure to the Windows clipboard for using it in another program.
Thick vector
In vector mode the image is drawn by thick lines.
Bond type
Toggles the drawing of bond types on and off. If on, single, double and triple bonds are drawn, and special bond types (aromatic, amides etc) are shown in different colours.
Atoms
If neither of the buttons are set, a vector model is drawn. First button: ball & stick model. Second button: the atom numbering within the molfile is shown. Third button: hetero atom symbols are shown in vector models. In 2D molfiles implicite hydrogens and atom aliases are addeed. In the latter cases the atom size buttons affect the font size.
Rotation and translation
Rotation, translation and zooming of the molecule is possible with the mouse when the cursor is in the graphics area. However, you may open the rotation or translation mode toolbar with the sel button and choose the increment of the rotation or the translation with the spin button. The arrow buttons select the direction of the movement about the x, y or z-axis. The More button enables the selection of advanced methods.
Atom info
At the bottom of the outer side bar the number of the current atom are shown, its symbol, type and coordinates. If the molfile contains partial or formal atomic charges, they will appear in red and green.
Cursor
The cursor buttons move the red atom highlight upwards or downwards. Alternatively, you may click the mouse on the selected atom.
Browse mode
If a multiple molfile was inputted in browse mode, you can browse forward and backward the structures in the file with these buttons. The Data button toggles the display of textual data in MDL sdf or rdf files.
Clean the window, reset graphics
This button is used to clear the dot surface representation of the central atom, initiated by the Proton-proton distances option of the main menu Utilities option.
Display toolbox
Displays the toolbox dialog of the graphical utilities.
Close toolbox
Closes the toolbox dialog of the graphical utilities.
Graphics area
This is the area for the graphical display of the molecule.
Status line
If available, displays the extended atom types, residue and chain info etc of the current atom. The results of some calculations of the graphical utilities may also appear here.
CA carbon atoms only
Sometimes PDB peptide files contain only the backbone CA carbon atoms. This file can be useful for example for displaying a simplified graphical representation of a peptide in a drawing program or multimedia application. Most modeling programs may behave oddly (HyperChem, Sybyl etc) when inputting such files, especially if bond connection information is not included. Mol2mol accepts such files and adds bonding information (although chemically the result is nonsense). If a high-end modeling program has problems with such a file, it may help if you (re)convert it to PDB or Sybyl mol2 format and try again.
MODEL
PDB files may contain several instances of the same structure, for example different conformers yielded by an NMR NOE structural elucidation or a molecular dynamics experiment. These are called models, in the file they are included between the MODEL and ENDMDL tokens Only a few modeling programs support the use of models.