Exorga, Inc. - Consultants in Chemistry, Molecular Modeling, and the Environment


StruMM3D (Version 8.0.0.X, 2016) © Vernon G. S. Box, Ph.D.


Tips and Shortcuts for Using The StruMM3D Molecular Modelers


A copy of the USER's GUIDE - STRHELP.PDF - for StruMM3D should already be in StruMM3D’s home directory ( \Str3Di ). The User's Guide supplied here can be downloaded. The file is viewable using any web browser, so you can read it, print it, or search it directly. Keep a copy in your \Str3Di directory/folder.

All the newer versions of StruMM3D initially look for the help file at the Exorga.com website (using your preferred web browser), and use that source of information, if you have an Internet connection going. If you do not have an Internet connection, then StruMM3D will use the help file that is present in the \str3di directory on your computer.

The newer versions of StruMM3D also detect whether the version you are running is the latest, and if not, will inform you to go download the newer version.

We have tried everything possible to work with Internet Explorer 8, but we have NOT been able to overcome some of the glaring deficiencies of that version, which include, most annoyingly, slow starts and slow loading of local (on your hard disk drive) html files. We are now using Internet Explorer 11 and, while IE8 really sucked, we can confirm that IE9 to IE11 REALLY rock, big time! If you do not have one of the versions IE9 to IE11 then get it now. They are fast, secure, and work very well with StruMM3D.

If you want to get back here easily and quickly, just create a bookmark for this page in your browser.

If you need some basic template structures, for use in creating more elaborate molecular models, remember that some are provided on the StruMM3D TEMPLATES page.

Click this link if you need a short tutorial on using the CONSTRUCTION options in StruMM3D to draw/create a molecule, (a PDF document).

Remember that StruMM3D will NOT display the energies of molecules that have missing Hydrogens, Lone Pairs, or other atoms. ALL of the valencies of ALL of the atoms must be satisfied before StruMM3D will assess its energy. Use the Main Menu > Construction routine to add Hydrogens and Lone Pairs, if you need to.

The INPUT/OUTPUT TEXTBOX is the lowest control on the StruMM3D main window. It is also called the I/O BOX. This is the place to enter commands, and parameters, from the keyboard, and where the program's hints and tips will be displayed. The text here is usually GREEN.

Want to “hear” something interesting? Save a bit of your favourite music, as a wav file, with the name moodmuzic.wav and copy this file into the \Str3Di folder. Now launch StruMM3D and enjoy the music. If the music doesn't start, then use the P environment toggle to switch it on or off.


StruMM3D's Hot Tips and Topics

Why do crystal strucrure data sometimes seems just wierd?
Moving the structure using mouse gestures
Associate StruMM3D With Your SXS, XXS, and Other Structure Data Files
Newer StruMM3D data files might not work in older versions, the easy fix
Drag and Drop Files into StruMM3D to Display the Data
Erase Str3disp.win, or Str3display.par, or str3display.dat if you have display problems
Does the displayed molecular model look a bit confusing, with weird bonding?
Use the molecule log to find structures you have saved
Auto-Save Your Structures and Keep Them
Always Draw At Least Three Atoms
The Advantages of Using Our Structure Drawing Routine
Link Templates into Big Molecules
Lost Your Molecular Model (off screen)?
Change Atom Types to Add New Layers of Structure
Helping FireFox and Internet Explorer to Run StruMM3D
Mousing About and Selecting Atoms
Auto-logging of Data
Manipulate Your Structure's Bit-Maps
The benefits of using SVGA, UVGA and XVGA graphics modes
MOVEMENT's Continuous Translation/Rotation
A Quick Way to Refresh/Redraw Your Model
Inexplicable Errors When Using Our File Conversion Utilities
Associate FileConv With Your Non-Str3di data Files
Automatically move selected dihedral angles into their minimum energy arrangements
Do you want to map the dihedral energy as you rotate a bond?
Find the lower dihedral energy minimum in a model that has two adjacent chiral centers
Minimizing Structure Energy of Models/Molecules
Structure Energy Minimizations of Highly Delocalized, Polyenoid, Molecules
Features of the structure energy minimization window
Energy minimization taking too long?
Energy Units?
Why do some bonds have different colours?



Why do crystal structure simulations sometimes seem just wierd?

The leading cause of wierd bonding in the simulations of molecular structures from crystal structure data arises because the experimenters have included in the atom coordinate data some disordered atoms. Instead of just one atom for the best position of the disordered atom, they include two, or three others, to represent the possible positions of the disordered atom.

StruMM3D doesn't get this information from the CIF file and thinks that there are really two, or three, atoms all clustered very closely to each other. Too closely. Worse, since StruMM3D does not erase any atom in a crystal structure simulation without permission, no matter how wierd the atom's position in the molecule is, the result is a really wierd looking/bonded structure.

The thing to do here, is to ask StruMM3D to review the structure data, and grant permission to delete all non-bonded atoms and all atoms that are too close to other atoms (well within normal bonding distances). Then the wierdness will be, at least partially, resolved.

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Moving the structure using mouse gestures

When the program is "idle" and a structure is onscreen, you can drag the cursor around on the screen (hold down left mouse button, followed by moving the cursor while the left button is still held down) and the structure will rotate in the same sense as the gesture. This feature works best with small molecular models. You can toggle this feature on, or off, by typing ~mg into the I/O BOX, followed by clicking IDLE or OK.

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Structure Energy Minimizations of Highly Delocalized, Polyenoid, Molecules

Occasionally, while minimizing the structure energy of highly delocalized molecules like carotene, and other polyenes, you might get weird data due to the assignment of unusual charges to allylic carbons. This can be corrected by toggling the environmental delocalization switch on. Normally, structure energy minimizations should be done with the environmental delocalization switch off.

We are investigating this odd program behaviour. The fact that the proper charges will be assigned for all atoms in these molecules, simply by adjusting the bond ranges of the delocalized bonds is a strong clue.

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Drag and Drop

If you like to “drag and drop” files onto applications to get things moving, then remember that StruMM3D doesn’t mind that at all. Just keep a shortcut/icon to StruMM3D somewhere on your desktop, where it is normally visible and have a good time “draggin ‘n droppin”. Remember that you can create a shortcut to StruMM3D by using the main menu item HELP.

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Erase Str3diplay.dat if you have display problems

If you have any problems that seem to be related to the way StruMM3D displays the molecular models, or the menus, or the various "daughter" windows, then close the program, go into the \str3didirectory and erase (delete) the STR3DISPLAY.DAT file, or any file named STR3DISPLAY for older versions. When you restart StruMM3D, the program will start up with the default view and you can then select/reconfigure the program parameters via the UTILITIES/PROGRAM PARAMETERS menu.

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Does the displayed molecular model look a bit confusing, with weird bonding?

When StruMM3D initially analyzes a set of atomic coordinate data, obtained by any experimental diffraction method, it will display all of the atoms in that data, even if they are single atoms, unconnected to any others, like the oxygens of water molecules.

If the structure looks cluttered or disorganized, the problem often occurs when the diffraction data is obtained at low resolution, or with significant experimental error in the measuring of atomic positions and the experimenters have included all of the possible positions for some atoms due to their measured disorder.

This is a signal that StruMM3D needs to perform its usual rigorous structure data analysis in order to display the best possible molecular structure.

If you are at the main/parent StruMM3D window, simply go to the main menu and select Structure/Review structure data. The structure will be redisplayed correctly. If you see this problem when the Query - Molecular Geometry - Movements window is open, then simply left double click on the STRUCTURE ENERGY (the purple) button in the Movements window.

If the atomic disorder is too great then the structure will require lots of doctoring to be useful, and you might best seek the molecular coordinate data from some other source.

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Associate StruMM3D With Your XXS, SXS, and other structure data Files

Download the batch file ASSOCSTR.BAT and use it from a command prompt. The syntax for usage is simply ASSOCSTR X:, where X: is the letter of the drive on which the STR3DI folder is found. This batch file will establish the usual StruMM3D file associations, or delete (ASSOCSTR X: /d) them if you wish. Remember that you must also have the app ASSOCIATE.EXE in the directory/folder from which you execute ASSOCSTR.BAT. Both files can be found on the download page.

Remember that if you have FileConv in your \Str3Di directory, then you can associate many more file types with StruMM3D. FileConv automatically determines, from the files extension, what kind of file you are seeking to convert (it recognizes the extensions – CIF, CMF, CSD, ENT, PDB, XYZ, M3D, MOL, MOP, ALC, MM2, MM3, MMX and SCH).

You can also establish these file associations manually. After you have installed the StruMM3D molecular modeling programs, open Windows Explorer and go to the \Str3Di\DATA directory. Now right click on any SXS file and a windows entitled "OPEN WITH" will appear. Following the instructions, ensure that the check box beside "always use this program to open this file" is checked, then you should click the "OTHER" button, and browse the \Str3Di directory to find StruMM3D. Now click on StruMM3D, so that it appears in the window beside "OPEN", and then click "OPEN".

Try to click on any SXS file to see if the program is run properly, displaying the structure you wish to see. If you get an error message telling you that the file's name is too long, then you will have to adjust the way Windows gets the file name. Just open Windows Explorer, click on TOOLS then FOLDER OPTIONS, or VIEW then FOLDER OPTIONS. Now select FILE TYPES and scroll down the list until you see SXS file , or StruMM3D SXS file. Now click on EDIT, in the next window click on EDIT again, then in the box that is entitled "Application used to perform action" remove the quotation marks from around the %1 symbol ( change "%1" to %1). You can also just erase the %1 symbol in Windows NT. Now you are ready to go looking at structures just by clicking on their file names.

Repeat this process for any XXS file in the directory \Str3Di\XRAY, and any other structure/file that you wish to be able to view with StruMM3D just by clicking on it, like MM2 and MMX files. These files will now be "associated" with the StruMM3D program, and whenever you double click on any of these XXS or SXS files, the WINDOWS operating system will launch StruMM3D and load the file into the program for you. Instant molecular modeling!

This file/program association is also the only step in "configuring" MicroSoft's Internet Explorer to recognize the StruMM3D program as a helper/viewer application. No other "tweaking" needs to be done to establish the association between IExplorer and StruMM3D.

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Use the molecule log to find structures you have saved

This feature will work best with Internet Explorer 9 - 11.

The MOLECULE.LOG is now one very powerful creature that can be searched from menu options within StruMM3D. It is specially created, automatically, whenever you open a new x-ray data file, or save any structure using the “Save As” option.

If you save a molecular model using the "Save As" routine - STRUCTURE/SAVE AS - then the program will prompt you for a file name and then a brief description of the molecule. These data will be saved into a HTML file - molecule.htm - which will be easily accessed if you have already associated the STR3DI file extensions - SXS and XXS - with StruMM3D. This file is automatically saved/stored/updated in the \str3di directory.

Associating the native STR3DI file extensions with StruMM3D is discussed above. It is important to associate your SXS and XXS files with StruMM3D.

For example, if you wish to recall the structure of one of your creations, just click on STRUCTURE/OPEN THE MOLECULE LOG and your preferred web browser will pop up the file molecule.htm. The display will show the file names and descriptions of all of the structures you have saved using the SAVE AS routine. The descriptions will actually be URLs (they will be underlined and highlighted like any Internet website’s URLs). If you are using Internet Explorer 9 (the new release candidate version), just by clicking on the appropriate URL (description) the structure will be displayed by StruMM3D.

If the structure/description you seek is not visible, then use the EDIT/FIND feature of your preferred web browser to locate the description. After you click on EDIT/FIND, your preferred web browser just asks for a keyword, which you will enter, and then will locate the entries having that keyword. F3 repeats the search until you find the desired entry. Then just click on the description URL.

This feature works just like the access you have to structures when you visit the STR3DI Molecular Models and Templates page at the Exorga, Inc. website. There, if you click on the name of a molecule (that is displayed as a URL), then StruMM3D opens and displays the structure. If you can’t get a structure at that site, then you need to associate your SXS and XXS with StruMM3D.

You would also have noticed that StruMM3D writes another file in keeping track of saved data - named molecule.log. This file is saved in a format that enables you to put the data on saved structures into a spreadsheet, or other database, program. This file is also automatically saved/stored/updated in the \str3didirectory.

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Helping Internet Explorer to Run StruMM3D

If you have associated the XXS and SXS files with StruMM3D, as we have strongly recommended, then, if you are using Internet Explorer the browser does it all for you. Automatically! No further user input is needed for this symbiosis! You will also notice that StruMM3D knows what your favourite browser is. You don’t have to do anything.

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Mousing About and Selecting Atoms

StruMM3D does not use double-clicking to identify or select atoms. In StruMM3D, the right-click is the equivalent of a double-click.

There are three types of occasions in which you will need to click on an atom -
1. to find out what the atom number/type is use a left click
2. to identify atoms in a "geometry" query use a right click
3. to identify atoms, at other times, as requested by the program, use a right click

If the program is not doing anything in particular, left-clicking, or right-clicking, on a vacant part of the screen does nothing. Double left-clicking on a vacant part of the screen prompts the program to "refresh", or redraw, the current structures, to clean things up, if you will.

If the program is idling, left-clicking on any atom will show the atom's type and number in the last/lowest rung of the information section -at the bottom of the screen.

StruMM3D will measure distances/bond angles/dihedral angles if you select, from the menu bar, Query/Geometry. You should then "single" left-click each atom in the pattern - two for a distance, three for an angle, four for a dihedral angle - the appropriate data will be displayed. Then left-click OK to get ready for the next measurement.

In nearly every other instance that the program will ask you to select an atom, you can either "single" left-click the atom and then left-click to confirm the selection by left-clicking OK, or you can “single” right-click the atom to select and confirm.

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Always Draw At Least Three Atoms For A New Structure

The first three atoms of any new structure must be coplanar and StruMM3D is especially set up to facilitate the drawing of those first three atoms. The program will allow you to draw a two atom unit, but there will be problems if you try to add hydrogens or lone pairs to that two atom unit. The routine that adds hydrogens and lone pairs to structures NEEDS at least three atoms in order to do a precise job.

For example, if you wish to draw methane, draw H-C-H. For ethane, ethene and ethyne, draw C-C-H, C=C-H and C#C-H respectively. Then use the routine to add hydrogens to all the atoms which unfulfilled valances.

The drawing routine has been carefully upgraded, and works very well, but you must remember to draw those three atoms for a new structure.

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The Advantages of Using Our Structure Drawing Routine

The structure drawing routine is very precise, and somewhat demanding, since it allows you to construct a molecule in precise geometric detail. Every feature of the molecule can be placed into the structure while in the drawing routine, from bond lengths, to bond angles, to dihedral angles. Very few molecular graphics programs allow the user such extensive control over the structure drawing process, most preferring to require the user to draw a crude 2-dimensional structure that the program then refines. Often stereochemistry at chiral centers is lost when using the 2D to 3D routines, but the structure you draw using StruMM3D will remain precisely what you wanted.

Another huge disadvantage to this 2D - 3D routine is the users inability to precisely alter small parts of well defined structures in a scientifically meaningful way. For example, let's say you have the x-ray structure of a naturally occurring alcohol, and you want to model the ethyl ether. if you use the 2-D drawing routine to modify the O-H group, you end up with an imprecise structure. In order to refine the new O-CH3 group, all of the structure must be run through a structure energy minimizer. a lamentable waste of time and resources.

StruMM3D enables you to do these careful, precise structural alterations, and to have a scientifically useful entity at the end of the process. The STR3DI drawing routine can be used as carefully, or laxly, as you wish, since you can override suggested data and use whatever values you wish. Of course, if you step beyond the bounds of propriety, then StruMM3D will scold you suitably.

At the end of the drawing process a piece of your molecular model might be off the screen. After you exit from the drawing routine, just double-left-click anywhere in the picture window and the model should be placed properly for viewing on the screen.

Learning to use the drawing routine eventually gives you very powerful control over your molecular modeling exercises.

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Change Atom Types to Add New Layers of Structure

Suppose you wish to convert a cyclohexane into an axially substituted ethyl cyclohexane, would you use the drawing routine? You could, but that would be the long way.

The easy way would be to convert an axial hydrogen into a carbon, using Construction/Change Atom, and then to add hydrogens onto the carbon, using Construction/Add H/lp. Now simply select one of the methyl's hydrogen and convert that into a carbon, to give the conformation you wish, and then use Construction/Add H/lp to complete the task, by adding all of the missing hydrogens.

You'll notice immediately that the program automatically adjusts the new bond length to the proper value. The routine to add hydrogens and lone pairs, Add H/lp, also does these additions in the context of the hybridization status of the central atom. Thus, for example, SP3 atoms get as many hydrogens or lone pairs as they need to be tetravalent.

This method of modifying a structure is fast, very intuitive, and can be applied to the construction of many interesting structural units, with great conformational control.

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Link Templates into Big Molecules

Linking established structure fragments, or templates, also provides a very fast and powerful method for constructing precise molecular models. This can be very rapidly demonstrated by linking two cyclohexane molecules into a decalin, and then adding a third cyclohexane to give a perhydrophenanthrene, or a perhydroanthracene.

This demo is easily done if we remember that the C1-C2 bond of the cyclohexane is parallel to the C4-C5 bond. So we'll put a cyclohexane on screen and arrange it for good visibility of the bonds we wish to manipulate. Then save this structure, and recall it, so that there are now two cyclohexanes onscreen. Now move the C1 of one molecule precisely over the C5 of the other, and the C2 of the moved molecule should overlap the C4 of the second. Now use Construction/Link to fuse these into a trans-decalin, remembering that StruMM3D will erase one of the overlapping atoms of each pair.

You can now, again, recall the cyclohexane, and similarly, or with some imagination, fuse this "new" cyclohexane onto the decalin to generate a larger entity. And so on .... Note that a very important aspect of the exercise is that the rotational orientations of the units have been kept constant, so ensuring that the geometric relationship of the units always remains the same.

Orient Structure

One of the other useful routines to remember is Movement/Orient Structure, which allows you to orient a selected pair of atoms, whether in a common bond or not, along the X-Axis of the screen. The "reference" atom is always placed at the same, predetermined, position on the screen, and the "relocatable" atom is placed along the X-Axis, to the left of the "reference" atom. The atom that will be used to measure dihedral angles in the drawing process will be attached to the “relocatable” atom, and will be in the same plane as the “reference” and “relocatable” atoms. The program will then enable you to place your next atom precisely where you wish, with reference to these three key skeletal atoms.

If you wish to overlap two bonds precisely, you can use these features of Orient Structure to do so. You should then rotate the pair of structures (A + B) through 90 degrees about the Y-Axis, using Movement/Translate/Rotate, and look along the common bond. In this way you can see if the newly formed dihedrals, or other aspects of the orientation of the pair of molecules are correct, BEFORE you Link them. If the relative orientation of the units is not good, rotate one molecule, A or B, about the Z-Axis centered on an atom in the common bond (along which you are now looking), until you have the correct features.

With a little practice, you'll be able to link very diverse units, as precisely as you wish, to make very complex molecules. You should also read the tip on Changing Atom Types to Add New Layers of Structure to get additional methods for rapid structure building.

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Auto-Save Your Structures and Keep Them

Nothing is worse than losing a structure after you have spent several minutes modifying it, or drawing it! The way to hedge against this unhappy event is to manually save the data frequently, File/Save, or to allow the program to automatically save the structure's coordinates each time it has been modified.

You enable the auto-save mode by going to Utilities/Program Parameters and left-clicking on the box for environmental variable "t" (temporary file write). Whenever the variable is in the uppercase, "T", the feature is active. If it is lowercase, "t", the feature is inactive. This command box is a toggle control.

The auto-save feature writes the data into a file called TEMP.SXS. This file is over-written at each save and so contains the latest changes to the structure. If you do something odd, or the program crashes, the simply load TEMP.SXS and you have the structure back!

Remember, this file is over-written frequently and so you should rescue any data you need from it as soon as you can.

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Auto-logging of Data

When QUERYing lone pair interactions or steric effects in a molecule, you are given the options of viewing the data onscreen, or having the data go to a LOG file, "auto-log".

The auto-log feature is really useful since the lone pair interactions and steric effects data are appended to a LOG file having the same name as the structure data file. Only the total values of the interactions are shown onscreen, a very rapid, almost instantaneous analysis, and the interacting centers are highlighted. Since each structure has a unique name, each LOG file will also be uniquely named and will be a collection of "properties/data" for that structure.

This same LOG file is used when you ask for the structure's coordinate/bond length data to be printed. Again, the data are appended. Not only will you get a "hardcopy" from the printer, but the data are all appended to the appropriate LOG file.

Thus, at any point in time you can go back to edit/use/read this log file in whatever way you wish, unhurriedly. This is great for report writing. In fact, the log is always written in the regular font "Courier" in order to facilitate the table-like format needed for presentations, and you can alter the font's size as you wish.

Be aware that the log files can be imported into a spreadsheet program, like EXCEL, and that allows you to view the data in a more organized fashion. You might have to remove the heading/title of the file.

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Manipulate Your Structure Images and Bit-Maps

If you have a structure onscreen, and you select Utilities/Copy To Clipboard, StruMM3D will put the image of the structure into the clipboard. You can the do many wonderful things with that image. You can paste it into a word-processed document. You can paste it into MS Paint in order to invert the colors, or to artistically convert it into a surreal image. Anything that comes to mind, and any operation that can be done with/on graphics images, can be done with the structure's image.

The molecular images in this web-site were generated in precisely this fashion!

The one thing to watch with the bit-maps created by StruMM3D is their size. A bit-map file can take up a relatively large space on your hard disk drive, though usually smaller than 1 megabytes. However, these files can be drastically reduced in size by pasting them into MS Paint, and re-saving them as GIF files. Be sure to "trim" or "crop" these images to remove some of the unused space from around the edges, and that will reduce the file size also.

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The benefits of using SVGA/UVGA/XVGA graphics mode

The most recent versions of the StruMM3D molecular modelers for Windows will work perfectly in either VGA (640 x 480), SVGA (800 x 600), or UVGA (1024 x 768), or XVGA(1280 x 1024) modes.

If you have an old VGA monitor that can only show a 640 x 480 screen, then in VGA mode, StruMM3D fills the screen and all of the "daughter" windows used by the program must be within the body of the picture/graphics screen. These "daughter" windows can sometimes interfere with your view of the molecular model, but you can always resize the model, or move it, in order to have an umimpeded view.

However, in SVGA/UVGA/XVGA mode, StruMM3D only occupies a part of the computer's screen and the StruMM3D window, and any "daughter" windows it generates, can be moved around on the DeskTop. Thus, the "daughter" windows can be moved off the StruMM3D window, onto the WINDOWS desktop, so providing total access to the StruMM3D graphics screen!!

The higher resolution of the SVGA/UVGA/XVGA mode also gives better bitmaps/images of your molecular models for incorporation into your "clipboard". The resulting printed image will be better than that obtained while working in VGA mode.

You can get the same "look/feel" for StruMM3D in XVGA mode as when it is in VGA mode by moving the StruMM3D window up into the top left corner of the screen. We tend to use the XVGA mode because of the convenience, even if we are using a small high-resolution (less than 15") monitor.

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Minimizing Structure Energy of Models/Molecules

Most of us have been mislead into believing that the three dimensional potential energy surface describing a molecule's geometrical/conformational features is a relatively smooth one, with well distinguished energy minima. While this might be true for a small molecule like methane, or ethane, it certainly isn’t true for a molecule of normal size and complexity, and even less so for chiral molecules. The temptation is usually to assume that the energy profile of a polyatomic molecule looks like that of a simple diatomic, like hydrogen, but that is far from true. So, rather than a steep and smooth surface, converging onto the minimum, most potential energy surfaces are, in fact, usually quite convoluted, with many local minima, and to make matters worse, they are often shallow and pocked in the regions of the local minima. Imagine looking at a very irregularly bounded hole in the ground whose surfaces have been eroded by heavy rain. That’s more like it.

The QVBMM force field, simply adjusts the positions of the atoms in the molecule (the atomic coordinates), allowing high energied interactions to "push and pull" these atoms into more stable positions, until a low energied structure is obtained. Just imagine dropping a marble onto each of these surfaces and allowing its potential energy to move it to the nearest metastable position, where it can become stationary. A steep and smooth energy surface will rapidly direct the marble (molecular model) to the nearest local minimum, or even the global minimum. A shallow, pocked surface will require many hours of exploration in order to find the "best" local minimum, and even more time to move the model to the global minimum.

When you put a crude structure into the QVBMM force field, within a few computational cycles the major features of the molecule, bond lengths and angles, at that local minimum, are established. Usually the QVBMM force field will keep searching for a better structure, but you can stop the routine at any time, especially if you know what the energy of the best structure is, or you observe that the energy of the current structure is not changing appreciably with each cycle of the QVBMM force field. You really do not have to wait while the QVBMM force field searches, especially if you don't need a VERY good structure, as might be the case if you are building a slightly complex molecule from templates.

Remember to change the MCM (Minimization Calculation Mode) value to suit your current molecular model. If you are minimizing the structure energy of a very crude molecule, or a very large molecule, then the MCM should be set to zero. Otherwise, set the MCM to 1, for the most rigorous minimization mode. In special cases, when minimizations of very large molecules take very long times, set the MCM to 2. How to set the MCM? When the program is idle, and the I/O BOX says so, type ~MCM N where N is the integer 0,1, or 2, as you need from the discussion immediately above. The ~ is important. No quotations.

In fact, the QVBMM force field was designed to allow you to stop the routine at any time in order that you might examine the structure of high energied entities on route to the local minimum you wish to observe. Suppose you make a model of gauche butane with a dihedral angle of 50 degrees and you want to see what the bond lengths and angles of THAT model would be, then simply run the model through ONE cycle of the QVBMM force field and stop the routine. The dihedral angle might no longer be 50 degrees, it most likely will be larger, but it won't be far from 50 degrees. Now you can look at that "snapshot" to see what the creature really looks like, and the data might surprise you. You definitely CANNOT do this using any other molecular modeling program.

You will have GREAT difficulty asking other force fields to allow you to look at high energied molecular models. If you are fast enough at hitting the "CONTINUE" button, you can stop the QVBMM force field routine, regularly and whenever you wish, in order to gain these intimate insights into the way angles and bonds change as the model moves towards its nearest minimum energy. After saving the "snapshot", you simply resume the structure energy minimization routine.

One note of caution. Occasionally we meet molecules, usually small molecules, which have trouble finding a minimum. Remember that there are various options that can be invoked when setting up the minimization (Special, Normal, Anneal), and occasionally, the simplest option “Normal”, rather than “Special” will produce a faster and better result. So if the “Special” mode fails, just use the “Normal” mode.

We have a written a small program that will enable you to use StruMM3D to minimize your molecular structural energies in batch mode. You run this program to set up the tasks, and then it instructs StruMM3D to minimize the structure energies of all the files you have specified, no matter how many, without you being there. It is called STR3DBATCH. We also have a set of batch (BAT) files to help you to minimize the structure energies of a bundle of files while you go see a movie, or go to the gym. These batch files are also not in the downloaded package, but you can get them for free, from Exorga. Just ask, by e-mail. We’ll also instruct you as to how you can make your own batch file.

Of course, once you are doing a batch minimization you don't have to be there while StruMM3D3 does its job. For people, like teachers who are handling a molecular modeling class, this is an excellent way to minimize the energies of a bundle of crude structures that were generated by a group of students, outside of class time, while you attend to other matters, or amuse yourself otherwise. Researchers or teachers can take a template, like tetrahydropyran, rapidly draw/fashion 20 monosaccharides, then minimize their energies while they are busy doing other things.

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MOVEMENT's Continuous Translation/Rotation

The MOVEMENT - Translate/Rotate windows has been revamped and some new features are now present. Foremost among these is the new "button" at the right the window that allows you to toggle between continuous and non-continuous movement by left-clicking on that button. The caption and colour of this button will change, each time it is clicked, between N for "non-continuous" and RED to C for "continuous" and GREEN. The "vertical button" on the left of that window will also trigger continuous motion if the other button is in the C - continuous - green mode.

Thus, if you want to rotate the model in a stepwise fashion, moving it only with each click of the mouse in the appropriate "direction" box, then ensure that the right button says "N" - non-continuous and is RED. If you click on that red button the caption changes to "C" - continuous - and the colour to GREEN, and now the next time you hold down the left mouse button while the pointer is on a "direction" box, that motion occurs smoothly and continuously. A great way to display and examine your model.

If the model is in continuous motion, the "continuous" button is GREEN, you can switch from one mode of motion to another - translate to rotate or vice versa - just by clicking on the appropriate translate/rotate button, and the model instantly responds. Similarly, all of the controls will work interactively when you are in "continuous" mode, and you can move the model in whatever motion mode, in whatever direction, just by clicking on the appropriate control button.

You can change the size of the rotation/translation unit by clicking on the appropriate "motion Unit" button. There is also a "textbox", with the cursor blinking in it, that you can use to input any other motion unit size you wish. If you actually change the number in that textbox, then the motion unit size is changed to that value immediately, and the textbox becomes green. If you wish to change the motion unit size from the start-up value of "1" (that button will be green), to that number present in the textbox, just double-click on the textbox, rather that retyping the already-present number. Upon double-clicking, the textbox goes green and the new unit becomes effective.

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Lost Your Molecular Model (off screen)?

Occasionally you will inadvertently move the molecular model off the screen, and you might have no idea where it is. Sometimes the program has simply positioned the molecular model in an awkward way on the screen and you don't have a full view of it.

There are a few ways to fix this small problem.

This will pop the structure back onto the screen, into view.

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A Quick Way to Refresh/Redraw Your Model

Occasionally you will have circles or lines drawn onto the molecular model and you might want to "clean up" the structure , to get rid of these extraneous markers.

If the program is doing nothing special, then simply double click on the picture window, OR select Structure/Review structure data from the main menu.

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Inexplicable Errors When Using Our File Conversion Utilities

Remember that FileConv will always be a “work-in-progress” since the guys that produce structure coordinate data files for other programs keep changing their formats, and some people create error-laden files. As soon as we are aware of a data format change, we try to update FileConv, so if you keep us informed, we’ll continue to ensure that the conversion utility is always up to date, but we have to contend with other people writing badly formatted data files.

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Associate FileConv With Your Non-Str3di data Files

If you have FileConv in your \Str3Di folder, then you should associate ALL molecular structure files with StruMM3D. Then when you are using StruMM3D and you click on a file that is not in Str3Di format, FileConv is launched automatically, it converts the file to Str3Di format and then StruMM3D will display the data.

The utility - FileConv - has replaced the older file conversion utilities that were used to convert coordinate data files from other formats into those used by StruMM3D. This utility is now very powerful and will process most of the commonly used coordinate data file formats. The utility is now tightly associated with StruMM3D, so that while you are running StruMM3D, you can now simply click on almost any coordinate data file (in most formats) and the simulated structure will be presented.

You can also use FileConv as a stand-alone app. FileConv automatically determine, from the files extension, what kind of file you are seeking to convert (it recognizes the extensions – CIF, CMF, CSD, ENT, PDB, XYZ, M3D, MOL, ALC and SCH, among others) if you "run" the program from the Windows Start/Run menu. MM2, MM3, MM4 files are already automatically handled by StruMM3D.

FileConv can be used to process each type of file individually, by clicking on the appropriate command button and following the simple instructions. FileConv can also process large numbers of structure data files in BATCH mode.

If you have FileConv in the \Str3Di folder/directory, then the simplest thing to do is to associate each of the above file types with StruMM3D, and by simply clicking on a file, the structure will be displayed by StruMM3D. If you wish to use FileConv as a stand-alone program, then associate the Str3Di files with FileConv as well. Clicking on the file should bring up a window asking for the program to use to “open” it.

On the other hand, if you do not wish to associate files with FileConv, then, if you select Windows’ Start/Run window and type into the textbox - e:\Str3Di\fileconv e:\Str3Di\data\whenever.m3d - the program will convert the file “whenever.m3d” into the StruMM3D format and store the converted file in the same e:\Str3Di\data directory, where the original file is present. Another way to use it is to simply right click on the structure file, click “open with” and search for, or select, FileConv.

While it is good to remember that FileConv is a “work in progress”, simply because other people that generate data for molecular modelers keep on changing their files formats, the current (2001) version 2.5.0.2 will handle almost any coordinate data file adeptly.

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Automatically move selected dihedral angles into their minimum energy arrangements

StruMM3D will automatically adjust some of the dihedral angles in your molecular model during structure energy minimization runs. To understand which dihedrals will be adjusted, we must look at the way the program classifies them.

All terminal functional groups that have one ot two non-hydrogen atoms in them - like methyl, ethyl, hydroxyl, amino, halogen - are automatically detected by StruMM3D and their dihedral angle data (atom numbers etc.) are placed into an array that we shall call the Dihedral Array. During structure energy minimizations StruMM3D looks into the Dihedral Array and automatically minimizes these dihedral angle energies, if you so desire.

You can also load dihedral data into the Dihedral Array by simply measuring these dihedral angles. You select Query/Geometry from the main menu and then, following the instructions, click on the four atoms in the dihedral. StruMM3D gives you the dihedral angle and enters the data into the Dihedral Array. You can select as many dihedrals as you wish. Again, during structure energy minimizations StruMM3D looks into the Dihedral Array and automatically minimizes these dihedral angle energies, if you so desire.

A third way to select dihedral angles and enter these into the Dihedral Array is to use StruMM3D's substructure searching routine. You select Query/Sub-Structure Search from the main menu and you will be guided into the use of the routine. Briefly, you will be asked to identify the TYPES of atoms, and their hybridization states, that will make up the dihedral angle. For example, octane has eight carbon atoms linked consecutively and if you identify atom 1 as C, atom 2 as C, atom 3 as C, atom 4 as C, then the program will ask which atom (of 1, 2, or 3) the atom 4 is linked to. You respond that atom 4 is linked to atom 3, so giving a straight chain rather than a branched chain. When StruMM3D sees that you want to identify a straight chain, it knows that you are looking also for the dihedral angle data. StruMM3D will then perform the search for that substructural unit and, if you had selected the option to store the data, StruMM3D will log the dihedral data into the Dihedral Array.

You can erase the data in the Dihedral Array by selecting Energy/Select Dihedrals For Minimization and then not bother to select any dihedrals. StruMM3D also allows you to select the option to minimize the dihedral energies during structure energy minimization, or not.

We have recently added a new feature to StruMM3D that allows you to perform a minimization of the dihedral angle energies alone, not during a structure energy minimization run. Suppose you have obtained some data for octane, but it is in a multiply gauche conformation and you want to have the anti-anti-anti-etc (stretched out zigzag) conformation form this model. Simply use the Query/Sub-Structure Search routine to log all of the C-C-C-C dihedrals into the Dihedral Array, and then select Energy/Minimize Dihedral Energies. StruMM3D then automatically adjusts the dihedral angles in a very interesting graphically stimulating routine.

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Do you want to map the dihedral energy as you rotate a bond?

Undoubtedly, the best way to do this is to create the conformations (many) of the molecule, each of which at one of the many conformational points along the way (of rotation), minimize the energies of these, plot the energies against the dihedral angle, and then invoke the best smooth curve to complete the graph. This way, at every point, the data are for the energy relaxed conformations. This will obviously be very time consuming and labour intensive.

If you just want a quick and approximate dihedral energy map for that dihedral, then use the Rotate a Bond routine by selecting Movement/Rotate a Bond. Follow the instructions for identifying the key atoms that compose the dihedral, and then click on the Dihed. Eng. Prof. button (Dihedral Energy Profile). StruMM3D will perform the desired operation and will log the data energy vs. dihedral angle into a file that starts with the molecular model's name. So butane.sxs will have its data logged into butane.log in the directory \Str3Di\data\logs.

I then just use a spreadsheet program (like MicroSoft's Excel) to graph the data. The exercise is visually stimulating and quite informative. However, you must remember that the graph is not an exact model of what you would expect if the structure/conformation of the molecule was energy minimized at each point on the graph, but it is close enough to give you some interesting data like approximate rotational barriers.

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Find the lower dihedral energy minimum in a model that has two adjacent chiral centers

Let us suppose that we are working with cis-1,2-dimethoxycyclohexane that you just created by modifying the structure/model for cyclohexane. The two methoxyl groups are in some random conformation and you want to use the Energy/Minimize Dihedral Energies routine to place these two methoxyl groups in their lowest dihedral energy arrangement. However, you know that there are two possible arrangements -

  1. the axial methoxy methyl can be engaged in a C-H hydrogen bond with the equatorial methoxyl's oxygen, or

  2. the equatorial methoxy methyl can be engaged in a C-H hydrogen bond with the axial methoxyl's oxygen

but you don't know which is more stable, and you want to use the Energy/Minimize Dihedral Energies routine to determine which is.

Well, just select Energy/Minimize Dihedral Energies from the main menu, and StruMM3D places the molecule into a low energy state. Notice that StruMM3D will always move one dihedral first. All you have to do is to change the conformation at the second dihedral either by swapping two groups on the oxygen atom (a lone pair and the methyl), or by using the Movement/Rotate a Bond routine.

Then repeat the Energy/Minimize Dihedral Energies routine. You will get a different minimum and now you can decide which is the lower minimum energy structure.

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Features of the structure energy minimization window

When you initiate a structure energy minimization process, a new window appears (Stereo-Electronic Energy Data) that shows all of the contributors to the strain energy of your molecular model. Each quantity of this dynamic display changes as the program approaches the desired minimum. There are two displays that can be useful if you want to stop the process prematurely, and these are at the bottom left of this Stereo-Electronic Energy Data Window.

The upper display, pale blue number on a white background, shows the current minimum energy of the molecular model. It has intentionally been programmed to show the energy in millicalories, so that if there are very small energy changes occurring, these can be viewed.

The lower display, black number on a variable colour background, shows the current energy of the last searched structure. This number goes all over the place! If the last searched structure is lower in energy that the current minimum, then the upper display's number will change and the lower display's background colour will flash red. There is no point stopping the minimization process when this display is flashing red, unless you really want to.

Sometimes the lower display's background flashes yellow, and that tells you that the last searched structure has an energy that is similar, or almost identical, to the current minimum. If the lower display flashes yellow frequently, with no red flashes, then we are close to the minimum, and usually not more that 5 to 10 calories away. Remember that at room temperature, a molecule in solution can get up to 16 kcal/mol of energy from collisions with the solvent. In its normal vibrational/rotational state, any molecule at room temperature will be much more than 10 calories above it's energy minimum. It takes quite a bit of searching of the conformational energy surface of any complex moelcule in order to strip away those 10 calories and place the molecule at it's energy minimim.

Sometimes the lower display's background flashes green, and that tells you that the last searched structure has an energy that is larger then the current minimum. If the lower display flashes green or yellow frequently, with no red flashes, then we are close to the minimum.

If you are in a hurry, or you think that you do not want the program to carry out as detailed a search of the conformational energy surface, as it normally will try to do, then you can stop the structure energy minimization process manually, when you see that the model’s current energy is changing slowly.

As soon as StruMM3D senses that the energy is changing only slowly, it will post a message telling you that it is safe for you to stop the structure energy minimization process manually. If you do, then you can only quote the energy to 2 decimal places (the third decimal place is highly uncertain and meaningless). After the message has been posted, the lower display flashes yellow and green frequently, with few, or no, red flashes. Thereafter it will always be a good time to stop the structure energy minimization process manually.

However, you can simply wait for the structure energy minimization process to end normally, but that may take some time, depending on the size of the molecule and the complexity of the contours of its potential energy's surface.

Registered users of StruMM3D can ask us how to exert further control over the speed with which StruMM3D will minimize the structure energy of their models.

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Newer StruMM3D data might not work in older versions, the fix

The recent updates to StruMM3D have put more date into the native format for x-ray diffraction derived coordinate files. Specifically, the last line in any file that has extension .XXS, .XLC, or .XCC, will have the original x-ray structure file name. If you are using an older version of Str3Di32 and you are having problems with these files, simply delete this last line and you should be back in business. In any event, it really is time to get StruMM3D.

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Energy Units?

The default energy units used in StruMM3D is kcal/mol. You can change that default to kJ/mol. This is not a change to take lightly, since StruMM3D stores the energy of each molecule in the data file, if the molecule is fully elaborated (all valencies filled and no structure errors).

To make sure you want to do this, then use your text editor to open the file Str3Display.Dat, which is located in the folder \Str3Di. Line 6 looks like "1,0,0,0", without the quotations. Change the 1 to a 3. Do not change anything else. Now the default energy units will be kJ/mol.

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Why do some bonds have different colours?

The normal two electron bond is shown by StruMM3D as a solid yellow line. It is usually tapered, with the thicker end of the wedge closer to the viewer (user), in order to accentuate the perception of depth. Single bonds are shown as one line, double bonds as two parallel lines and triple bonds as three parallel lines. Transition state single electron bonds and two electron bonds are shown as dashed lines and are usually single bonds.

The red transition state bond will represent a two electron bond that will be broken during a structure energy minimization process, while the dark green transition state bond will represent a two electron bond that will be formed, made into a full bond, during a structure energy minimization process.

The single electron transition state bonds encountered in the norbornyl cation are usually only found in very fragile transition state organic molecules at low temperatures. They are also found in stable organometallic complexes like the metallocenes and other metal - pi-molecular systems. These bonds are represented as yellow dashed transition state bonds, that will remain dashed and yellow when they have been relaxed to their most favourable length by a structure energy minimization process.

StruMM3D lets you know, or asks you, when you are working with a one, or two, electron bond.

Occasionally you will encounter a pi-system in which delocalization is interrupted by a single bond, whose Pauling bond order is very close to 1.5. A Pauling bond order of 1.5 is the borderline between single and double bonds. In other words, if this single bond was a shade shorter it would complete the chain of delocalization so creating an extended pi-system. This situation is often met when working with molecules simulated from their crystal structure data.

If StruMM3D determines that these "borderline single/double bonds" could really be double bonds, within the limits of the experimental error for the determination of bond lengths in that diffraction experiment, then it will designate these bond as double bonds. These "borderline" double bonds will be represented as "peach puff 3" coloured solid bonds. If you measure their lengths, StruMM3D will show you their StruMM3D and Pauling bond orders.

This is what the environmental toggle "D" does when invoked manually, but now StruMM3D also intervenes and will automatically flag these borderline bonds for you.

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To find out more about STR3DI's support programs jump to THE StruMM3D MOLECULAR MODELERS