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Graphics window

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Click the part of the Graphics window you want to know more about.

Graphics window

 

Utilities available from the Graphics window

Utilities of the graphics window

Click the button you want to know more about.

 

Atom-atom distances:

You are prompted to select two atoms. The distance of these atoms will be displayed in the message window and the side tool bar.

 

Distances to nearest neighbours:

In the bottom status line the distances to the nearest neighbour atoms appear automatically. The default value of the distance limit is 1.8 Angstrom. You can change it in the second Preferences window. Yellow bonds will also emphasize these atoms (this does not apply when the axes are drawn)

 

Bond angles:

The bond angle defined by three atoms is calculated. The angle between these atoms will be displayed in the message window and the side tool bar.

 

Dihedral angle:

The dihedral angle as defined by four atoms is calculated. The dihedral angle will be displayed in the message window and the side tool bar.

 

Dihedral angle of two planes/ring:

Dihedral angle of planes

The program prompts you to define the two planes by specifying three or more atoms in each. The best fitted mean planes and their angle are calculated. The two planes may contain common atoms (e.g. two spiro rings). As two planes define two angles, one obtuse and one acute (the sum being 180 degrees), the program calculates both and displays them in the message window. (Previous Mol2Mol versions used exact planes defined by three atoms.)

 

Distance from a least-square plane/centroid:

Select at least three atoms to define the plane. Press Enter after marking the last atom. Finally, click on the base atom outside the plane. Mol2Mol provides two approaches to this calculation. Each has advantages for different types of structure. Select whichever is more appropriate for the current structure:

a)  A plane is fitted to the selected group of atoms by a least-squares procedure, and the distance of the base atom from this plane is calculated.
b)  The centroid of the atom group is calculated, and the distance of the base atom from this centroid is determined.

Distance from plane 1. Distance from plane 2.
The best fit plane is shown in yellow. It remains visible until the button is released.

 

Pyramidality:

You are prompted to enter the numbers of the three atoms of the base plane, followed by the out-of-plane atom. Pyramidality has several definitions, therefore four different indicators are calculated:

Pyramidality a.

a)  The distance d of the out-of-plane atom from the plane defined by the three other atoms (altitude of the pyramid). Note that the altitude of the pyramid depends on the bond lengths, so this is not an exact measure of pyramidality.


 

Pyramidality b.

b)  The deviation of the sum of the three angles around the central atom from 360 degrees is independent of bond lengths. This measure is insensitive to small pyramidality.


 

c)  A new definition of pyramidality is index P, as described by Radhakrishnan and Agranat (Struct. Chem. 2, 107-115 (1991)). The magnitude of P varies between 0 and 1.0 (e.g. it is 0.77 for nitrogen in ammonia with bond angles of 109.4 degrees), and is positive, if viewed from the central out-of-plane atom and the order of the other atoms is clockwise. P is valid only if the bond angles are 90 < Q < 180.

 

Pyramidality d.

d)  The pi-orbital axis vector (POAV) defined by Haddon (J. Amer. Chem. Soc. 112, 3385 (1990) is set to have equal angles with the three sigma bonds. This angle theta (or 90-theta) is also a good measure of deviation from planarity. It is 90 for planar systems, 101.04 for the ball-shaped buckminsterfullerene and 108.9 for a tetrahedral carbon atom.


 

Planarity and puckering of rings:

Puckering of rings

Click on an atom of a 5-9 membered ring (if the atom belongs to more than one ring, the program prompts to click on another atom to identify the ring). The program calculates a best fit plain to the atoms, as well as the following geometrical data:

 Geometric and puckering data of the selected ring:
 
    Atom:    Distance from the     Distance if the actual atom is
            least-square plane:       excluded from the plane: 

    C(9)      -0.280 .   max              -0.676 .
    S(8)       0.276 .   max               0.844 .   max
    C(4)      -0.239 .                    -0.588 .
    N(1)       0.091 .   min               0.207 .   min
    C(12)      0.151 .                     0.382 .
 
  SUM dev^2:   0.493
 
  Ring dihedral angles:
    C(9) S(8) C(4) N(1)                    36.600
    S(8) C(4) N(1) C(12)                  -26.803
    C(4) N(1) C(12) C(9)                   -3.105
    N(1) C(12) C(9) S(8)                   31.218
    C(12) C(9) S(8) C(4)                  -41.015
 
  The sum of the ring dihedral angles is   -3.104

The distance of each atoms of the ring from the best fit plane is calculated by two methods: the current atom itself is included in the calculation of the best fit plane, or not. The atoms having the maximum and minimum amplitude (distance from the plane) are marked by max and min. The sum of the squared distances from the ideal plane and their average are also calculated, as measures of ring puckering. Finally, the endocyclic torsion angles of the ring atoms are also calculated.

The best fit plane is shown in yellow. It remains visible until the button is released (manually or automatically, as set in Preferences).

 

Remove atom:

Use this option to remove an atom from the molecule. The program will prompt for the atom to be selected. You can use this option for instance to remove dummy atoms from a molecule, if they were not automatically removed during the input.

 

Change atom:

On clicking an atom, you will be prompted to enter the new atom symbol. If the current molfile uses extended atom types (Alchemy, Sybyl, Hyperchem, PCmodel, Moby, MacroModel, Cache), you will have to supply the extended atom types as well. These atom types will be checked to see whether they are valid in the current molfile. If they are not valid, a warning will appear asking whether the change is to be accepted or rejected.

 

Change bond connections or types:

If you select the Change bond type button from the upper menu bar, the side bar will be replaced by another set of buttons to enable the selection of the appropriate bond type. First select the bond type (1-2-3, 0 to clear the bond, ar for aromatic, am for amide, du for dummy, unk for unknown, no for no-connection, co for coordinative, io for ionic and w for weak), then click on the two ends of the bond. Only use bond types, which are allowed in the target file type.

When a crystal coordinate, Cartesian or Z matrix file is loaded into the program, Mol2Mol generates a connectivity table for it. If the file contains inaccurate geometry, the program may generate "dummy" bonds between the atoms, or some necessary bonds will not appear. If this happens, use this option to add or remove bonds, or change the bond types.

The screen will be re-drawn after changing the bond type, when the button is released. Alternatively, press any button which forces a screen re-draw.

 

Add hydrogen atoms:

While with the main Edit | Add hydrogens option you can add all of the hydrogen atoms to a molecule at once, this option adds the hydrogen(s) only to the selected atom. In automatic mode, Mol2Mol determines automatically the number of hydrogens and the geometry of the newly created center. When you select another button from the side menu bar, the program enters into force mode: the atom and bond types, bond lengths are not taken into consideration, but some necessary basic geometric conditions.

 

Add formal charges:

Use this option to add/remove formal charges to/from atoms. You are prompted to click on an atom, then right-click and select the appropriate formal charge (-3 +3).

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Colouring and selecting parts of the molecule or the assembly:

coloring * If the inputted file consists of more than one models, chains or residues (see multiple files), with the aid of these three buttons the parts can be coloured differently for better visualization. If all or part of the structure(s) is coloured during the conversion to the POV-Ray format, these colours will be used in the generated POV-Ray file.

selection * If the inputted file consists of more than one models, chains or residues, or contains helix, sheet and/or turn info, use these three buttons to select them for better visualization. Clicking with the mouse on an atom will toggle the selection. In the case of a simple molecule the residue button selects the whole molecule. If a whole structure or part of it is selected during the conversion to the POV-Ray format, it will be coloured according to the atoms, with the colour of the selection, or according to the atomic charges, if the input file contains them (or any other atom property from a data file).

selection If a Brookhaven PDB file contains alternative locations (more than one instances of the same atom), this button is also available and by using it the alternative locations will be selected and displayed in different colors (alternative locations can be removed via the Utilities | Peptide/DNA utilities | Remove alternative locations menu option).

If the selection mode is active, a new pop-up menu opens when pressing the right mouse button.
   Reverse selection (toggle): This deselects the current selections and selects the previously unselected structures or moieties.
   Show only selected (toggle): Only the selected atoms will be shown. This may help if atoms of the molecule are too close and overlap, and selection is difficult. If part of the molecule(s) are hidden, this will be taken into consideration when generating POV-Ray files.
   Fix selection (toggle): If in this selection mode you click on an atom, part of the structure(s) will be selected or deselected. This makes the use of different utilities impossible. By fixing the selections, the selections made so far remain unchanged, when clicking the atoms using on of the utilities.
   Show not peptide/DNA molecules too (toggle): (available only in backbone mode) Show those chains, or molecules too, which do not belong to the backbone.
   Reset: This clears all selections.

Coloring by chains

 

Coloring by residues

 

Right-click menu

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On residues, subunits, models and multiple files:

Structure of files

* The majority of molecule files describe really one molecule only (even if this is for example a coordination complex). Some molfiles may contain more tahn one molecules, like PCModel, Xmol, MXYZ and certain crystal structure files. These molecules may be completely different, or they may contain for example different conformers of the same structure.

* More advanced files possess multiple levels of structural information: residues in biopolymers (like amino acids in the proteins, nucleosides in the nucleic acids or other embedded moieties) represent the first (lowest) level. Residues are simple to treat, because all of the programs supporting residue information handle these elements in the same manner. Of the supported molfile formats PDB, Sybyl mol2, Insight car, HyperChem hin, MacroModel and SHELX files contain residue information. When interconverting between these formats, this information will be preserved and written into the new file.

* In fact, a peptide or nucleic acid is often an assembly of several molecules called chains. PDB, Sybyl mol2, Insight and MacroModel support chain information. In HyperChem chains are treated as independent molecules.

* Finally, these advanced molfiles may contain several molecules (meaning now the whole assembly, such as a peptide or nucleic acid plus water molecules, ligands etc). In the case of PDB files these are named models. Such files are referred to as multiple files throughout this document. When using PDB files it is assumed that models have the same primary structure, differing only in their conformation (as a result of MD experiments or structure determination by NMR). In Sybyl mol2, Insight and MacroModel they can be totally different structures too. To the contrary PCModel, Xmol, MXYZ, SDF and several X-ray files contain only this utmost level info, but no residue or chain information.

* As a consequence, this multilevel structural information can only be moved into a new file format between Sybyl, Insight, MacroModel and PDB. When transforming into HyperChem format, the utmost level cannot be preserved, and when converting into PCModel, Xmol and MXYZ xyz files the chain and residue information will be lost.

* To make things more intricate, the same structure (assembly) will not be treated on the same way by different programs, for example the structural water in proteins: when writing a structure in PDB file format, water molecules are formally treated by some programs as one chain consisting of several water "residues", by other programs as independent chains or molecules.

Mol2mol offers several ways for inputting multiple structural files and convert the whole file or only part of it into multilevel format or "all into one". Experiment with the sample files in the mol2mol/other folder:



  pdb1fja.ent       PDB file of actinomycin  DNA complex, with three models
  1cfc_ca.pdb       PDB file with ten models, contains only the CA backbone atoms
  oxytocin.pdb      oxytocin molecule in PDB format
  oxytocin.hin      oxytocin molecule in HyperChem format	
  macromodel.out    MacroModel file with three conformers of an adamantoyl glycopeptide	
  pcmodel.sst       PCModel file with four different componds


 

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Multiple file conversion

Some file types (Brookhaven PDB, Sybyl mol2, MacroModel, Insight car, PCModel, Xmol, MXYZ) may contain multiple instances of the same structure, differing only in their conformations, for example the results of a molecular dynamics experiment. In this case a multiple-to-multiple or multiple-to-many file conversion is possible by selecting this check box of the Open file window. After inputting the first structure and converting it to the desired file, the forthcoming structures will be read, converted and appended automatically.
multi1 multi2

Molecule file with multiple instances of the same structure. Multiple conversion results in a similar file. As the indicators in the upper status bar show, the workplace now contains 3 models (molecules), 12 chains and 102 residues altogether.

Indicators
Input and conversion of one structure only.

Among the supported file types Brookhaven PDB files signal only clearly this type multiplicity: the presence of MODEL and ENDMDL tokens means that the same structure is present in multiple instances. In this case you will be prompted to read in only the first structure or the whole file. If you select the latter similar multi-structure output files will be automatically produced during the conversion in the case of Sybyl, MacroModel and Insight types. Conversion to Xmol xyz, Mxyz and PCModel results in a similar multiple file, but without the residue and chain information. In the case of HyperChem model information is lost, but residue and chain info is preserved.

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Summary of different input and output modes

* The basic and most used mode is to select simply a molecule file from the input window. The file is inputted and is ready for further manipulations.

* Batch mode (many-to-many) is for selecting several input files (of different types) and convert them to several files of the same output type in one run. batch mode
* The merge mode (many-to-multiple) is available (Save window} only if several input files were selected as in the case of batch mode. This is an amalgamation of batch and multiple modes: after the conversion the selected input files are unified and outputted as one multiple file of several independent structures. merge mode


The following modes are intended for the files containing more than one structures (molecules). Depending on the type of the input file, these can be absolutely independent from each other, or they are variations of the same structure (e.g. the result of an MD experiment). Sometimes a "molecule" is an assembly of several molecules (for example peptid chains and water molecules) Multiple files

selection dialog * If the All option is available, you may input all or select only several of the molecules.

* Otherwise you can select and input one molecule at a time.

* Alternatively, the browse mode is available: the first structure in inputted, and then you can browse the others from the Graphics window (the Data button is available only in the case MDL sdf or rdf files and toggles the display of associated data in the text window).

* Multiple-to-multiple mode: an input file with several structures will be transformed into another multiple structure file. Multiple mode.

* The split mode (multiple-to-many) is available (Save window} only if a multiple file was previously inputted in multiple mode: instead of writing one new file with several structures, each one will automatically be written into a new file (the opposite of merge mode).

Tabular summary of multiple files and their available modes

File type: Structural levels:*
Molecule/
Chain/
Residue
Selection: Multiple input Multiple write, split and merge modes Browse
mode
in normal input in multiple input  level 

 Sybyl mol2 M/C/R all or selected M no 1 yes yes yes
 Insight M/C/R all or selected M no 1 yes yes yes
 MacroModel, Maestro M/C/R all or selected M no 1 yes yes yes
 PDB M/C/R all or selected M/C yes 2 yes yes yes
 HyperChem M/R all or selected M no 1 yes yes yes
 PCMODEL M one selected no 1 yes yes yes
 Xmol M all or selected no 1 yes yes yes
 MXYZ M all or selected no 1 yes yes yes
 MDL SD M one selected no 1 yes yes yes
 Cambridge MODEL M one selected no 1 yes no yes
 Cambridge FDAT and
 MODEL
M one selected no 1 yes no yes
 Multiple CIF (CIF/MIF) M one selected no 1 yes no yes
 Beilstein's Rosdal M one selected no 1 yes no yes
 Free format Z-matrix and
 Cartesian
M one selected no 1 no no no

* Assembly or molecule complex: if an enzyme molecule consists of several peptide chains, structural water etc
** If only one molecule is inputted and it is an assembly, its components can be inputted independently too. Currently applies only to models in PDB files.

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Connectivity and bond types

Some molecules files, like most crystallographic files, Z-matrices or most of the PDB files, do not contain connectivity information at all. In this case Mol2mol will generate the connectivity matrix (bonds) using the standard covalent atom radii and valences. In the case of unusual valences, distances or bad geometry there may be mistakes in the created molecule. You can correct these in the Graphics window.

In addition, in most formats "natural" bond orders are used: 1, 2 and 3. In high-end modelling programs, having a built-in force-field or another advanced modules, other bond types (aromatic, amide, complex etc) are also used, designated usually with numbers greater than 3. Drawing programs may use a number of other types (bold, up/down wedged, hashed etc), cf. summary of stereo bond types.

Colouring of the different bonds in the graphics window (in high or true colour modes):

1-2-3whiteoooo
amidecyannnnn
aromaticwater greennnnn
complex light magenta nnnn
ionicyellownnnn
weakorangennnn
dummypinknnnn
no connection pinknnnn
unknownpinknnnn

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Conversion of special bonds

Cu-complexInput structures containing complex bonds (Cache, MacroModel, PCModel), ionic or weak bonds (Cache) can be converted from group-2 to group-1 files easily. Alternatively, you could convert the complex bonds into single bonds or remove them altogether. With upward conversions, if the target program does not support these bond types and you choose the conversion to single bonds, the program may present some warning messages about unusual atoms, but this should not affect the target structure. If you choose to remove the complex bonds, the target modelling program may detect unconnected lone atoms and display error messages. The Cu-complex in the sample file, PCMOD.PCM, (the fourth structure) contains complex bonds. Try experimenting with it.

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Summary of stereo bond types

The following table illustrates the special stereo bond types in ISIS mol, PLT, ChemDraw ct, ChemDraft and Rosdal files. Their interconversion from one file format into another is possible, if an appropriate matching type can be found.

bondtypes Stereobonds displayed

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Summary of supported program molfiles

		Atom	Atom 	Bond   Dummy  Lone   Default    Multiple    Chains,
		types	symbols	types  atoms  pairs  extension  Structures  Residues

ALCHEMY		x		123mad	x	x	MOL
SYBYL		#	#	123madn	x	x	SY2,MOL2  x		x
ISIS mol		x	123(a)s x	x	MOL
ISIS sdf		x	123(a)s x	x	SDF	  x	
CSSR			x	1	x		CSS
DTMM			x	1	x		MOL
MOBY		x		(123a?) x	x	MOL
Insight		#	#	123a	x		CAR	  x		x
MacroModel	x		123cd	x	x	OUT	  x		x
Maestro		x	x	123cd	x	x	MAE	  x		x
Cache		#	#	123ciw		x	CSF
HyperChem	x		123a	x	x	HIN, HCS  x		x
PCModel		x		123c	x	x	PCM	  x
Z matrix		x		?		Z
Cartesian		x		?	?	CAR
CACAO			x				IN
PDB		#	#	1iw*(?)		x	PDB, ENT  x		x
ROSDAL			x	123			STR	  x
ChemDraft		x	123s		x	DAT
MOPLO			x	1			XYZ
ChemWindow mol		x	123a			MOL
Xmol			x				XYZ	  x
MXYZ			x	123		XYZ	  x
CIF			x	1			CIF
CIF/MIF			x	123a			CMF	  x
FDAT			x	1			DAT	  x
MODEL			x	123a			MDL
SHELX			x		x		SHX, INP
PLUTO			x	1	?		INP
PLT			x	123s	x	x	PLT
WIMP			x	123	x	x	FTR
SCHAKAL			x	1			DAT
ChemDraw CT		x	123s	x	x	CT
POV-ray			x	any	x	x	POV
UltraMol (MolPic)	x	123a			MP3
Molecules 3D		x	123aw		x	M3D

	a	aromatic bonds
	m	amide bonds
	n	no connection
	c	complex bonds
	d	dummy bonds
	i	ionic bond
	w	weak bond
	s	several stereo bond types are used (wedged, hashed etc)
	*	for standard residues connectivity is not necessary
	?	depending on the version
	#	both atom types and symbols are used
In a few programs atom numbers are used instead of atomic symbols (6 for C, 8 for O, etc)

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Summary of coordinates, rotation and translation methods

The program handles two coordinate systems parallely: world coordinates (coordinates of the molecule file, these can be seen in the side bar) and screen coordinates (to display the molecule). When the Show axis option is enabled, the displayed axes corresponds to the world coordinate system. If the molecule is rotated with the mouse, only the screen coordinates change. Although the molecule seemingly rotates, actually the camera (= your eyes) moves around the molecule.

Screen rotation
→ → →
Simple rotations and translations:

Simple rotation or translation with the mouse or by using the rotation sidebar changes the screen coordinates only.

Simple translation is never applied to the world coordinates.

    If you want to apply the rotation to the original coordinates, do one of the followings:

a) From the Preferences 1 option dialog select the Write rotated coordinates radio button. Only the outputted coordinates are changed, not within the program.

b) Select the Apply rotation to world option from upper button bar in the graphics window. The original coordinates are changed within the program.

 

Advanced, special rotation and translation modes:

    Centering methods from the upper button bar:

Center menu
  1. The geometric centre of the molecule is shifted to the middle of the screen;
  2. The currently selected atom (with the red cursor on) is shifted to the middle of the screen (same as the Jump button in the side bar). Useful in the case of big molecules before zooming in: the atom in question will not shift out from the window.
  3. The original (world) coordinates of the molecule are changed so that the origin of the coordinate system (0,0,0) is shifted to the centre of mass. The graphical window parameters are also reset. If the original molecule is not centred, after some operations (adding hydrogens) it may seemingly disappear from the work space. Use this option in this case. Its use is also advantageous prior to some operations, for example before the conversion to POV-Ray or other drawing program files.
  4. The currently selected atom (with the red cursor on) is shifted to the origin of the coordinate system (0,0,0). In addition, this atom will be placed in the middle of the graphics window.
  5. The original (world) coordinates of the molecule are changed so that the origin of the coordinate system (0,0,0) is shifted to the geometric centre of the molecule (into the centre of the bounding box). The graphical window parameters are also reset.

In the case avarage organic molecules the results of 3. and 5. are nearly the same. However, if the molecule contains one or more heavy atoms (Br, I etc) the difference can be profound. Experiment with the sample molecule TRIANONE.MOL.

Methods 3. and 4. are available from the main menu Utilities | Center molecule too.

    Centering and rotation methods from the rotation side bar:

   If you press the More button of the above rotation toolbar, new options appear:

More rotations
  1. The currently selected atom (with the red cursor on) is shifted to the Y axis. The distance from the origo will be the same as the original y coordinate of the atom (shifting parallel with the XZ plane).
  2. The currently selected atom is shifted to the Y axis. The distance from the origo will be the same as the original distance of the atom from the origo.
  3. The selected atom is rotated into the Y axis (oblique rotation).
  4. You are prompted to select three atoms. The first atom is shifted into (0,0,0) and the molecule is rotated so that the second atom lies on the Y axis and the third atom in the XY plane.
  5. You are prompted to select two atoms. The molecule will be rotated so that the connecting line of the two atoms will be parallel with the Y axis. The firstly selected atom will retain its original coordinates.

These 5 options always change the world coordinates!

The current state of the coordinate systems is reflected by the indicators in the upper status bar of the main window. Red lights reflect that the word and/or screen coordinates have been changed.

By combining these methods, many transformations can be applied on the molecule. For example, if you want to rotate a given bond parallel to the X axis:

  1. Rotate the bond parallel to the Y axis by using the above last option;
  2. Switch back with the Basic button, set the degree of rotation to 90 and apply Z rotation;
  3. Press the Apply rotation to world button (as 2. affects only screen coordinates).

Do not manipulate world coordinates, if it is important to retain them unchanged

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