Str3Di32 (Version 5.2.0.X, 2010) © V. G. S. Box, Ph.D.
Tips and Shortcuts for Using The Str3Di32 Molecular Modelers
All the newer versions of Str3Di32 initially look for the help file at the Exorga.com website (using Internet Explorer), and use that source, if you have an internet connection going. If you do not have an internet connection, then Str3Di32 will use the help file that is present in the \str3didirectory.
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 can say, without reservation, that Internet Explorer 8 truly sucks, big time!
A copy of the USER's GUIDE - STRHELP.HTM - for Str3Di32 should already be in Str3Di32’s home directory ( \Str3Di ). The User’s Guide supplied here is a self-extracting zipped file that will generate STRHELP.HTM when it is opened/run. The file is viewable using any web browser, so you can read it, print it, or search it directly. If needed you can download a copy here.
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 Str3Di32 TEMPLATES page.
Click this link if
you need a short tutorial on using the
CONSTRUCTION options in Str3Di32 to draw/create a molecule, (a Microsoft
Word document), or here for the document
in PDF format.
Want to “see” something interesting? Save a bit of your favourite music/wav file with the name moodmuzic.wav and copy this file into the \STR3DI folder. Now launch Str3Di32.
Str3Di32's Hot Tips and Topics
Associate Str3Di32 With Your SXS, XXS, and Other
Structure Data Files
Newer Str3Di32 datafiles might not work in older
versions, the easy fix
Drag and Drop Files into Str3Di32 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, NetScape and Internet Explorer
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?
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.
If you like to “drag and drop” files onto applications to get things moving, then remember that Str3Di32 doesn’t mind that at all. Just keep a shortcut/icon to Str3Di32 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 Str3Di32 by using the main menu item HELP.
Erase Str3disp.win, or Str3diplay.par, or Str3diplay.dat if you have display problems
If you have any problems that seem to be related to the way Str3Di32 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, or STR3DISPLAY.PAR, or STR3DISP.WIN for older versions, file. When you restart Str3Di32, the program will start up with the default view and you can then select/reconfigure the program parameters via the UTILITIES/PROGRAM PARAMETERS menu.
Does the displayed molecular model look a bit
confusing, with weird bonding?
When Str3Di32 initially analyses 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. However, sometimes there are problems with the data, and a confused structure, with weird bonding patterns will be displayed. This glitch often occurs when the diffraction data is obtained at low resolution, or with significant experimental error in the measuring of atomic positions.
This is a signal that Str3Di32 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 Str3Di32 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.
Associate Str3Di32 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 Str3Di32 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 Str3Di32. 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 and SCH).
You can also establish these file associations manually. After you have installed the Str3Di32 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 checkbox 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 Str3Di32. Now click on Str3Di32, 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 Str3Di32 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 Str3Di32 just by clicking on it, like MM2 and MMX files. These files will now be "associated" with the Str3Di32 program, and whenever you double click on any of these XXS or SXS files, the WINDOWS operating system will launch Str3Di32 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 Str3Di32 program as a helper/viewer application. No other "tweaking" needs to be done to establish the association between IExplorer and Str3Di32.
Always Draw At Least Three Atoms For A New Structure
The first three atoms of any new structure must be coplanar and Str3Di32 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.
The drawing routine has been carefully upgraded, and works very well, but you must remember to draw those three atoms for a new structure.
Use the molecule log to find structures you have saved
The MOLECULE.LOG is now one very powerful creature that can be searched from menu options within Str3Di32. 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 filename 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 Str3Di32. This file is automatically saved/stored/updated in the \str3didirectory.
Associating the native STR3DI file extensions with Str3Di32 is discussed above. It is important to associate your SXS and XXS files with Str3Di32.
For example, if you wish to recall the structure of one of your creations, just click on STRUCTURE/OPEN THE MOLECULE LOG and Internet Explorer 7 will pop up the file molecule.htm. The display will show the filenames 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) and just by clicking on the appropriate URL (description) the structure will be displayed by Str3Di32.
If the structure/description you seek is not visible, then use the EDIT/FIND feature of Internet Explorer 7 to locate the description. After you click on EDIT/FIND Internet Explorer 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 Str3Di32 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 Str3Di32.
You would also have noticed that Str3Di32 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.
If you recently upgraded to version 2.003.03.E, you might have established quite a collection of data in your “old” molecule.log file. You can copy/transfer this data into the new molecule.htm file by downloading the utility - LogToHtm - saving it into the \str3didirectory, and running it (clicking on it) there, AFTER you have run the version 2,003,03.E at least once to establish the molecule.htm file. This issue obviously does not arise if you are using a more recent version of Str3Di32
Helping FireFox, NetScape and Internet Explorer 7
Internet Explorer 7
If you have associated the XXS and SXS files with Str3Di32, as we have strongly recommended, then Internet Explorer 7 does it all for you. Automatically! No further user input is needed for this symbiosis!
FireFox
If you use FireFox for your routine web browsing, as many of us do, then you will have to ask FireFox to view the Exorga Website in Internet Explorer 7. You simply go to the appropriate web page, then click on the main menu “TOOLS”, then at the bottom of the window, click on “ALWAYS VIEW THIS PAGE IN IE”. As soon as we find out how to adjust FireFox’s repertoire of recognized file names, we’ll post a better solution here.
NetScape
Setup
NetScape is now an orphan program, and is no longer being developed. We recommend that you go use either IE or FireFox. However, if you like NetScape and want to continue to use it, then follow the instructions below.
Get your NetScape up and running, and then click successively on - Options, then General Preferences, then Helpers.
In the scrolling listbox headed "File Types", scroll down to "application/Octet-Stream" and click on that entry. Click in the box "File Extensions", and erase the current file type of EXE and BIN, then type in "SXS,XXS" (without the quotation marks). Now, in the "Action" button group, click on the "Launch the application" button. Then type in the full path name to the Str3Di32 program - for example c:\Str3Di\Str3Di32, or "browser" your way to the program via the Windows-Explorer-Like window, click on the program, click "open".
Now go back to the "File Types" listbox, scroll farther down, almost to the end of the list, until you see "text/plain", click on that entry, and follow the instructions given above. Here, of course, you will replace file extensions "TXT,TEXT" with "SXS,XXS".
Restore
We recommend that you put the settings back to their original values after each WWW molecular modeling adventure. Thus, for the application/octet-stream entry you should convert the file types back to EXE,BIN and for the text/plain entry you should convert the file types back to TXT,TEXT.
If you do not restore the NetScape settings, then be warned that when you are web browsing other non-Str3Di32 sites with NetScape, clicking on any hypertext link that is to a "plain text", or an EXE, or BIN file will launch Str3Di32.
We are trying to get NetScape to help us with this small inconvenience, but until then, NetScape users should plan to access the Option/General Preferences/Helpers feature at the start and end of a molecular modeling exercise.
Mousing About and Selecting Atoms
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
2. to identify atoms in a "geometry" query
3. to identify atoms, at other times, as requested by the program
If the program is not doing anything in particular, clicking on a vacant part of the screen does nothing. Double 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, 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.
Str3Di32 will measure distances/bond angles/dihedral angles if you select,
from the menu bar, Query/Geometry. You should then "single"
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 click
In nearly every other instance that the program will ask you to select an
atom, you can either "single" click the atom and then click
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 Str3Di32 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.
Str3Di32 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 Str3Di32 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-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.
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 Str3Di32 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.
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 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.
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.
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.
Manipulate Your Structure Bit-Maps
If you have a structure onscreen, and you select Utilities/Copy To Clipboard, Str3Di32 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 Str3Di32 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. We use the utility "ImageView" to do these jobs.
The benefits of using SVGA/UVGA/XVGA graphics mode
The most recent versions of the Str3Di32 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, Str3Di32 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 umimpede view.
However, in SVGA/UVGA/XVGA mode, Str3Di32 only occupies a part of the computer's screen and the Str3Di32 window, and any "daughter" windows it generates, can be moved around on the DeskTop. Thus, the "daughter" windows can be moved off the Str3Di32 window, onto the WINDOWS desktop, so providing total access to the Str3Di32 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 Str3Di32 in XVGA mode as when it is in VGA mode by moving the Str3Di32 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.
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. These potential energy surface 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, rather than steep and smooth. Imagine looking at a very irregularly bounded hole in the ground whose surfaces have been eroded by heavy rain. That’s more like it.
Since the QVBMM force field, simply adjusts the positions of the atoms in the molecule (the atomic coordinates), allowing high energied interactions to "push" 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 INPUT TEXTBOX 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.
We have a written a small program that will enable you to use Str3Di32 to minimize your molecular structural energies in batch mode. You run this program to set up the tasks, and then it instructs Str3Di32 to minimize the structure energies of all the files you have specified, no matter how many, without you being there. It is called STRBATCH. 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 STR3DI323 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.
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 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 - contiuous - 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 prsent 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.
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.
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.
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. 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.
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 Str3Di32. Then when you are using Str3Di32 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 Str3DI32 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 Str3Di32. 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 Str3Di32, so that while you are running Str3Di32, 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) if you "run" the program from the Windows Start/Run menu. MM2, MM3, MM4 files are already automatically handled by Str3Di32.
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.
The simplest thing to do is to associate each of the above file types with FileConv and by simply clicking on a file, it will be automatically converted into Str3Di32 format.
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 Str3Di32 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, orselect, 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 version 2.5.0.1 will handle almost any coordinate data file adeptly.
Automatically move selected dihedral angles into their minimum energy arrangements
Str3Di32 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 Str3Di32 and their dihedral angle data (atom numbers etc.) are placed into an array that we shall call the Dihedral Array. During structure energy minimizations Str3Di32 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. Str3Di32 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 Str3Di32 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 Str3Di32'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 Str3Di32 sees that you want to identify a straight chain, it knows that you are looking also for the dihedral angle data. Str3Di32 will then perform the search for that substructural unit and, if you had selected the option to store the data, Str3Di32 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. Str3Di32 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 Str3Di32 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. Str3Di32 then automatically adjusts the dihedral angles in a very interesting graphically stimulating routine.
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). Str3Di32 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.
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 -
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 Str3Di32 places the molecule into a low energy state. Notice that Str3Di32 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.
Features of the structure energy minimization window
When you initiate a structure energy minimzation 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 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.
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 almost sure to be at 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 not changing. Just wait until the lower display flashes yellow frequently, with no red flashes. This is a good time to stop the structure energy minimization process. However, you can simply wait for it 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 Str3Di32 can ask us how to
exert further control over the speed with which Str3Di32 will minimize the
structure energy of their models.
Newer Str3Di32 data might not work in older
versions, the fix
The recent updates to Str3Di32 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, .XCL, or .XCC, will have the original x-ray structure filename. 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.
To find out more about STR3DI's support programs jump to THE Str3Di32 MOLECULAR MODELERS