StruMM3D (Version 9.0.0.x, 2020) © 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 PDF apps like Foxit or Adobe, and by any web browser, so you can read it, print it, or search it directly. Keep a copy in your \Str3Di directory/folder. The help file is constantly being reviewed and updated, so 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, StruMM3D will inform you, download the update archival file for the newer version, and install it if you had used the StruMM3DX file to launch StruMM3D.
The INPUT/OUTPUT TEXTBOX, is the lowest control on the StruMM3D main window. It is also called the I/O BOX. There is a label to the left side of the box to point out its location. This is the place to enter commands and parameters using the keyboard, and where the program's hints and tips will be displayed. The text here is usually GREEN. The label for indicating the I/O Box also carries valuable information, and it is well worth your time to glance at it occasionally.
StruMM3D sometimes disables it's main menu in order to do some "housework". When you move the mouse point/cursor to the menu bar nothing gets highlighted and the menu does not respond. If you find that your main menu is disabled, and you want to work, just type ~ menu in the I/O Box and hit return/enter. It should give you back access. The tilde is important.
The list of topics below is NOT arranged in any specific order, this was done intentionally. We have found that by doing so, a reader will "browse" each header while searching for the desired one, and will be induced to read topics that he/she had not intended to. The supermarket does this to you too, and it works.
If you want to get back here easily and quickly, just create a bookmark for this page in your browser.
StruMM3D's Hot Tips and Topics
0 - StruMM3D's Handling of Non-native Files, Like CIFs
1 - Why do some bonds have different colours, and some atoms more than one colour?
2 - Use the \Str3Di\Projects Folder for Storing Coordinate Data From Your Projects
3 - Best Folder to use for Examining Imported CIF/PDB Files and Libraries
4 - What energy units are displayed by StruMM3D?
5 - What is the contribution of a given atom to the stereo-electronic strain energy in a molecule?
6 - Entering data when prompted?
7 - Name data files wisely, and delete them carefully
8 - Getting info from the original data file
9 - Why do crystal structure data sometimes seems just weird?
10 - Moving the structure using mouse gestures
11 - Associate StruMM3D With Your SXS, XXS, and Other Structure Data Files
12 - Newer StruMM3D data files might not work in older versions, the easy fix
13 - Drag and Drop Files into StruMM3D to Display the Data
14 - Erase Str3Disp.win, or Str3Display.par, or Str3Display.dat if you have display problems
15 - Docking? A few point to remember when planning to dock two molecules
16 - Use the molecule log to find structures you have saved
17 - Auto-Save Your Structures and Keep Them
18 - The Advantages of Using Our Structure Drawing Routine
19 - Using templates or Building a Molecular Model From Scratch
20 - Link Templates into Big Molecules
21 - Lost Your Molecular Model (off screen)?
22 - Change Atom Types to Add New Layers of Structure
23 - Helping your browser to Run StruMM3D
24 - Mousing About and Selecting Atoms
25 - Auto-logging of of Stereo-electronic Interaction Data
26 - Manipulate Your Structure's Bit-Maps
27 - MOVEMENT's Continuous Translation/Rotation
28 - A Quick Way to Refresh/Redraw Your Model
29 - Inexplicable Errors When Using Our File Conversion Utilities
30 - Associate Str3DiFileConv With Your Non-Str3Di data Files
31 - Automatically move selected dihedral angles into their minimum energy arrangements
32 - Do you want to map the dihedral energy as you rotate a bond?
33 - Find the lower dihedral energy minimum in a model that has two adjacent chiral centers
34 - Minimizing Structure Energy of Models/Molecules
35 - Structure Energy Minimizations of Highly Delocalized, Polyenoid, Molecules
36 - Features of the structure energy minimization window
37 - Energy minimization taking too long?
38 - Energy Units?
39 - What would the Pauling Bond Order be?
40 - A Special Note on Mn, Fe and Co Complexes
41 - How do I prompt StruMM3D to tidy up the file system?
42 - What's the best way to open a library of files?
43 - Launch StruMM3D from the Molecular Graphics Thumbnails
44 - Mood music for StruMM3D?
StruMM3D's Handling of Non-native Files
In the old days Cambridge Crystallographic Database (CCDC) CIF files used to be given alphanumeric names, like ZUXNAI10, and then the CCDC started to move towards numbered CIF files, their deposition numbers. The Crystallography Open Database (COD) also uses numbered CIF files, having similar name lengths to the CCDC CIF files. So if one wished to use the original file name as a way to access the file online and hence it's literature data, then there are several problems.
Whenever StruMM3D encounters one of the old CCDC alphanumeric CIF file names, during data importation, it will look in the CIF for the deposition number, and rename the file CCDC_deposition_number.CIF. So a recent CCDC version of the CIF for ZUXNAI will have the deposition number 1317422 in it, and so StruMM3D will rename this CIF file as CCDC_1317422.CIF. This sometimes happens also with CIFs downloaded from the iUCr, and there are many instances of oddly named CIF files that contain CCDC deposition numbers. COD files are left with their numeric names intact and so are not confused with the CCDC deposition numbered files.
Many users have been puzzled by this file name changing feature in StruMM3D. They start an exercise with a CIF, ABCDEF.CIF, and try to find the converted file's data (to native StruMM3D format) using the same starting name, but cannot find the files, since it has been converted to some format like CCDC_ABCDEF.CIF. If the file data conversion was successful you will see the molecule's image and you can rest assured that the new data file will be there.
StruMM3D will display the structure embedded in a CIF file, for example from the CCDC named 12345678.CIF, after the file conversion process has occurred the StruMM3D parent window title will show the current, and new, name, CCDC_12345678.XXS. This name will also be used to store the data in the appropriate StruMM3D folder, in native format, and location. The original CIF file name would also have been converted into CCDC_12345678.CIF.
The worst thing that can happen is when a CIF file has no coordinate data in it. Then StruMM3D will eventually tell you that the file, in native format, cannot be found, after it has searched high and low for it.
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What energy units are displayed by StruMM3D?
It is important to remember that StruMM3D was initially designed as a teaching tool for undergrads and grad students. The stated purpose was to enable us to examine and determine only the stereo-electronic strain energy of a molecular model, and then to ascertain whether this review further enabled us to understand the physical and chemical properties of the molecule. If the strain energy accounted for all, or most of, the observed molecular features, chemical and physical, then one could confidently state that there were no significant underlying delocalization factors like, n-sigma* effects, involved in the determination of the molecular structure or its properties. Thus, the validity of evoking obscure quantum chemical effects and fractional bonding to rationalize the structure/chemistry of the molecule would be questionable.
On the other hand, if the physical and chemical properties of the molecule cannot be fully rationalized by invoking only stereo-electronic strain factors, then this would validate the notion that quantum chemical effects must be involved and must be used to rationalize the structure/chemistry of the molecule.
StruMM3D has always had the ability to determine tha approximate delocalization energy in any truly delocalized pi-system in its molecular models, but this feature was not publicized. Now, this feature has been made available by usng the environmental command ~ cde 1 (to enable) ~ cde 0 (to disable) either at the Data I/O BOX, or by appending it to the StruMM3DComLine.Dat file.
Remember that StruMM3D will NOT display the energies of molecules that have missing Hydrogens, Lone Pairs, missing atoms, or atoms that are obviously erroneously sited. ALL of the valencies of ALL of the atoms must be appropriately satisfied before StruMM3D will assess a molecule's energy, a fully elaborated molecule. Use the Main Menu > Construction routine to add Hydrogens and Lone Pairs, if you need to. Molecules that are fully elaborated will visually display a lot more colour coded information that those that are not.
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What is the contribution of a given atom to the stereo-electronic strain energy in a molecule?
Often simple molecules show high stereo-electronic strain energy and it would be informative to be able to identify the total contribution to the overall stereo-electronic strain energy by any selected atom. This feature is quite informative when working with congested molecules.
The local strain energy at any selected atom in the molecular model can be made available by usng the environmental command ~ localstrain 1 (to enable) ~ localstrain 0 (to disable) either at the Data I/O BOX, or by appending it to the StruMM3DComLine.Dat file.
Whenever the program is idle, it says so on the command button bottom right, just click, one or twice, on any atom and its total strain energy will be displayed.
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Entering data when prompted
Whenever StruMM3D needs input from you it will display a prompt, or a hint, asking that you to provide it. The prompts and hints are always displayed in the horizontal labels that run all the way across the screen below the picture display window. There are two of these labels and below these is a text box, the Data I/O BOX, into which you can type information. At the bottom right there is a stack of small, shorter, labels, for StruMM3D suggested values or answers, adjacent to the prompt labels and the Data I/O BOX.
StruMM3D will usually display possible answers, or values, in the small rightmost labels, or suggested values boxes. The topmost of these suggested values boxes is special, and is coloured a very pale green. This box contains the default response, that will be used if you simply hit, or click on, OK, or ENTER.
If you are prompted for data and values appear in the suggest data box, and if you simply click on OK, the value in the topmost, green, suggest data box will be automatically used. If the data or value that you wish to use is in another suggested value box, then click on that box, and then click OK. If the data, or value, you wish to use is not displayed in any of the suggest data boxes, and StruMM3D thinks you can provide alternate data (and will indicate this by changing the colour of the Data I/O BOX to the pale green, and the colour of the adjacent label to its left), you will then be allowed to type it into the Data I/O BOX.
Whenever StruMM3D wishes to simply alert you to some event, or give you information to which no inputted response is required, the topmost, pale green suggested value box will become red, with the word INFO in it.
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Name data files wisely, and delete them carefully
It is important to know that hwenever you use StruMM3D to erase a data file it erases all of the data files that are associated with that name. So, for example, very often you will have a structure data file named ABCDE.sxs and you might modify that structure and save the new structure as ABCDE1.sxs, or ABCDE_1.sxs, or whatever, etc.. If you ask StruMM3D to delete ABCDE.sxs, then it will delete all of the "children" of that sturcture, the entire family ABCDE1.sxs, or ABCDE_1.sxs, or whatever, as well, because these children can be seen to be grouped into the family ABCDE*.*, from the Microsoft file naming rules. However, if you ask StruMM3D to delete ABCDE_1.sxs, then it will delete all files matching the pattern ABCDE_1*.sxs, but not ABCDE.sxs.
When StruMM3D cleans the house it really does a thorough job, and ALL of the targetted files are removed, regardless of the file extensions, even the graphics files.
Obviously, if you wish to ensure the safety of the parent ABCDE.sxs, then after loading ABCDE.sxs you will save it as ABCDE_1.sxs. Then play with this structure, ABCDE_1.sxs, to your hearts delight, and if you wish to erase these experiments you simply delete ABCDE_1.sxs. In this way, you can create several sub-families of ABCDE.sxs and delete them entirely if you do not wish to keep, or re-use, them, while keeping the parent structure safely.
As a safety net, if you ask StruMM3D to erase ABCDE_1.sxs, then StruMM3D will save this parent structure data file, ABCDE_1.sxs, into the folder \Str3Di\deleted, while it removes all the other family members from the PC. So, if you made a mistake you can go retrieve this parent and rebuild, if you need to.
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Getting info from the original data file
If you are working with coordinate data from an external source (for example a CIF, or PDB, data file), and the structure is already loaded/displayed by StruMM3D, you might wish to look at the file contents to view some type of information, like the name the authors gave to the molecule.
Instead of leaving the programme to find and use File Explorer to then find and display the text in the file, simply click on the little label captioned "I/O BOX" that is to the leftmost of the lowest labels on the working window. StruMM3D will then automatically open the appropriate file so that you can read the text.
This only works for imported data.
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Why do crystal structure simulations sometimes seem just weird?
The leading cause of weird 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 other atoms, to represent the other possible positions of the disordered atom.
StruMM3D does 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 weird the atom's position in the molecule is, the result is a really weird looking/bonded structure.
When StruMM3D initially analyzes a set of atomic coordinate data, especially those 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. These structures will normally have extensions .XXS and be generated from CIF, PDB, or other diffraction data. StruMM3D is not that generous to it native .SXS file. It immediately erases all misplaced atoms, or unbonded atoms, unless you take special steps to prevent that.
If you are at the main/parent StruMM3D window, simply go to the main menu and select Structure/Review structure data. StruMM3D will ask if you want to delete atoms that are too closely sited to others, or are unbonded. Once you decide the structure will be redisplayed correctly. All .XXS files so treated will have their extensions converted to .DXS, to differentiate them from unprocessed diffraction, .XXS, data. If you see this problem when the Query - Molecular Geometry - Movements window is open, then simply left double click on the STRAIN ENERGY (the purple) button in the Movements window.
If the atomic disorder is too great then the structure will require lots of tinkering to be useful. First, try to look at the CIF to identify and remove the disordered atom's ghosts, and if that does not help, then might best seek the molecular coordinate data from some other source structure determination, and hope.
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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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Docking? A few point to remember when planning to dock two molecules
Docking two molecules usually involves bringing two oppositely charged atoms, or a positively charged atom and a lone pair, close enough together to enable the electrostatic forces to influence the molecular cluster. This could also involve the juxtapositioning of two similarly charged atoms, or lone pairs, when the interaction will be repulsive, rather than attractive.
These atoms, or lone pairs will be peripheral entities, and certainly not within the bosom of the molecule where they will be heavily shielded from outside interference by van der Waals forces. So, if you want to dock two alcohols by hydrogen bonding, you are going to use the hydrogen on one unit to dock with the lone pair on the other. In this arrangement, the hydrogen will also experience the negative charge on the oxygen.
If you try to dock the hydrogen on one unit with the oxygen of the other then "things" will get in the way and unintended steric and van der Waals interactions will mar the process. It really is hard to get two fully substituted, non-bonded, nuclei to approach each other because of these steric and van der Waals interactions. That is why Sn2 reactions have significant activation energies, and why Sn1 reactions have lower, but finite, activation energies.
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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 Str3DiFileConv in your \Str3Di directory, then you can associate many more file types with StruMM3D. Str3DiFileConv 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. MIcrosoft, in its lack of wisdom, has not seen it fit to enable Windows Edge to have the same kind of access to the Windows file association features as Internet Explorer does. Internet Explorer 11 is wonderful for StruMM3D.
The MOLECULE.LOG is a very powerful feature that can be searched from menu options within StruMM3D. It is specially created, automatically, whenever you open a new 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. 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 Windows Edge or Internet Explorer, even though they might not be 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, 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.
Occasionally you might be forced to save a molecule but to omit putting any key words into the molecular log. It might be that the IUPAC name is a challenge, or some other reason. If, eventually, you want to put in some key words into a log entry, the you can use the update key words menu item under the STRUCTURE sub-menu. We have also made it easier for you to recognize molecules that have not been saved to the molecule log with key words. When these minimally documented molecules are in memory, and the program is idle, the I/O Box background will become a pale magenta colour.
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. Molecule.log is also automatically saved/stored/updated in the \Str3Di directory.
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Helping your browser to Run StruMM3D
StruMM3D will use any active web browser it finds. We use both Windows Edge and Google Chrome on our machines. StruMM3D automatically uses Edge when it is trying to run a molecular modeling exercise after searching the StruMM3D molecular log and the user clicks on a structure's URL. StruMM3D also automatically uses Chrome, if it is the default browser, when looking for help, when a CIF/PDB file search is done (since the browser opens the CIF/PDB file only for reading its contents), and when StruMM3D is looking for content.
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 and uses that browser when it is appropriate. 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 -
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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 precisely 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 conversion" routines, but the structure you draw using StruMM3D will remain precisely what you wanted, bond lengths, bond angles and dihedral angles, especially when drawing unusual structures.
So, you have to think carefully about what you want to construct and the sequence. This drawing routine is definitely not designed for a non-chemist. You need to know about, and understand, the importance of bond lengths, bond angles and dihedral angles, because you need to construct your molecular model so that the program recognizes each addition and uses it to guide you to the next.
The most significant disadvantage to a "2D to 3D conversion" 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 methyl ether. if you use the 2-D drawing routine to modify the O-H group, you end up with an imprecise structure since you have no control over the 2D program's initially imposed bond length, bond angle or dihedral angle. In order to refine the placement of the new O-CH3 group, all of the structure must be run through a structure energy minimizer. If the molecule is large then we have 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 StruMM3D drawing routine can be used as carefully, or laxly, as you wish, since you can override suggested data and use whatever values for bond lengths, angles and dihedrals, 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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Using templates or Building a Molecular Model From Scratch
Imagine trying to construct an airplane using Legos. You have to plan the build, because each three dimensional feature has a precise relationship with the others, and the whole target model. You cannt get there by randomly putting any sized Lego blocks anywhere and hoping for the best. You have to decide the sequence of addition, the size of the block needed, and precise positioning, of each each Lego block. This is the way, and the mindset to build a molecular model with StruMM3D.
The primary rule for using template structures to construct new molecular models is that you fill all of the valencies, of all of the atoms, before you proceed. Put in all of the missing hydrogens, lone pairs, lone electrons, etc, by using StruMM3D's construction feature. Once that is done, you can rapidly construct anything by simply substituting different atoms for one already present, in an appropriate fashion, while rapidly building to the desired target.
After each wave of substitutions, it is best to re-ensure that all valencies are satisfied. StruMM3D then allows you to exercise absolute control over the model's stereochemistry, bond lengths and dihedral angles when you most need to.
If you are constructing a molecular model from scratch, 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 precision 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 StruMM3D construction routine to add hydrogens to all the atoms which have unfilled valences.
The drawing routine is always being carefully upgraded as we always try to make it easier to use. It works very well, but you must remember to draw those three atoms for a new structure.
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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. For strained systems, especially strained ring systems, you must approach this exercise with craft and cunning because the final step must bring ring atoms close enough to bond..
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Link Templates into Big Molecules
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. Otherwise ask us, since we have an impressive array of structure coordinates, from diffraction (x-ray) studies, that can be used as molecular templates. Follow this link if you need a short tutorial on using the CONSTRUCTION options in StruMM3D to draw/create a molecule, (a PDF document).
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.
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
Few things are 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. StruMM3D will save the new file into the \STr3Di\Temp folder, so as to not overwrite your original data, and give the file ABCD.sxs a new name like ABCDE_temp.sxs.
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 Stereo-electronic Interaction 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.
Another option is to select LogVw, Log and View, from the option menu, and you will be shown each and every stereo-electronic interation of the type you are interested in, while the data is also being logged. It could take some time, but it is highly instructive.
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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 image will also be saved into the current working directory/folder, into the Str3Di storage folder and into the \Str3Di\Graphics folder.
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. JPG files are small but BMP files are much larger. A bit-map file can take up a relatively large space on your hard disk drive. Use the JPG as the default if you can, but remember that the default can be reset to BMP files..
The clean up utility TidyStr will also enable an automatic conversion of all of the .BMP files into .JPG files as is described below
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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 with all modern monitors, or with older ones 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 unimpeded 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 relatively smooth, U or V shaped, with well distinguished energy minimum. While this might be true for a small molecule diatomic molecule, 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, bumpy, and cratered in the regions of the local minima. Imagine looking at a very irregular bowl whose maker rushed the job of making it and left it to sag at the sides while sitting on an irregular surface before it hardened. 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, type ~ MCM N where N is the integer 0,1, or 2, as you need from the discussion immediately above.
The tilde ~ 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 "text box", 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 text box, then the motion unit size is changed to that value immediately, and the text box 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 text box, just double-click on the text box, rather that retyping the already-present number. Upon double-clicking, the text box 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.
Click on Movement/Position an Atom then enter 1, or whatever atom number you select.
Click on Movement/Translate-Rotate. In the new window click on JUMP and then click on a spot in the middle of the screen.
If the program is idling, then simply double_click on the picture window.
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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 idling, 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 Str3DiFileConv will always be a "work-in-progress" because the guys that produce structure coordinate data files for other molecular modeling programs keep changing their formats, and some people simply create very error-laden files.
As soon as we are aware of a data format change, we try to update Str3DiFileConv, so if you keep us informed, we'll continue to ensure that the conversion utility is always up to date, but we have to continue to contend with other people writing badly formatted data files. Maybe these non-StruMM3D data files are too complex and too long?
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Associate Str3DiFileConv With Your Non-Str3Di data Files
If you have Str3DiFileConv 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, Str3DiFileConv is launched automatically, it converts the file to Str3Di format and then StruMM3D will display the data.
The utility - Str3DiFileConv - 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 Str3DiFileConv as a stand-alone app. Str3DiFileConv 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.
Str3DiFileConv can be used to process each type of file individually, by clicking on the appropriate command button and following the simple instructions. Str3DiFileConv can also process large numbers of structure data files in BATCH mode.
If you have Str3DiFileConv 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 Str3DiFileConv as a stand-alone program, then associate the Str3Di files with Str3DiFileConv 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 Str3DiFileConv, then, if you open the Windows’ Start/Run window and type into the text box - 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, Str3DiFileConv.
While it is good to remember that Str3DiFileConv 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 184.108.40.206 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 energyas 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. StruMM3D will also draw a graph of the data, which will be saved in the "graphics" folder.
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 -
the axial methoxy methyl can be engaged in a C-H hydrogen bond with the equatorial methoxyl's oxygen, or
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.
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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 global energy minimum, which is meaningless if you are modeling solutions.
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.
When 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 data 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 update and to get StruMM3D.
StruMM3D users can now add any information they desire BELOW the last line of any of a StruMM3D native file (XXS, or SXS) to help them with their record keeping. StruMM3D will ignore this additional info.
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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 that first 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, and some atoms more than one colour?
StruMM3D is now a visual, highly intelligent tool, equipped with very sophisticated structure analytical algorithms, designed for molecular modeling and for reviewing the diffraction data gathered from organic and inorganic molecules. The development of StruMM3D has always been guided by the wish to have the programme independently and intelligently identify interesting, if not unusual, structural features and to visually draw these to the attention of the user. The user can then manually examine these features if it is so desired. To achieve this, bonds and their are explicitly depicted and van der Waals interactions are identified. Any atom that has bonding that is not the "normal" two electron type, found in the simplest molecules created from the elements of ithe first 3 rows of the periodic table, can have more than one colour. For example, the sulfur atom in a simple thioether is yellow, but that in thiophene is violet.
Single bonds are always shown as one line, double bonds as two parallel lines and triple bonds as three parallel lines. The normal two electron bond is shown by StruMM3D as a solid yellow line, if the bond order is greater than or equal to 0.95, as a solid pale green line, if the bond order is less than 0.95 but greater than 0.5, or as a dashed line if the bond order is less than 0.5. The bond line is usually tapered, with the thicker end of the wedge closer to the viewer (user), in order to accentuate the perception of depth, and this is true for all the other bonds.
Transition State bonds have bond orders less than 0.5. 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 bond that will be broken during a structure energy minimization process, while the dark green transition state bond will represent a bond that will be formed, made into a full bond, during a structure energy minimization process.
The single electron transition-state-likr bonds encountered in the norbornyl cation are usually only found in very fragile transition-state-like 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.
When the bond status is uncertain, StruMM3D will let you know, or asks you, if 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, but less than, 1.5. A Pauling bond order of 1.5 has traditionally represented the borderline between single and delocalized 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.
StruMM3D uses a different method for determining bond orders and StruMM3D's bond orders will often not match the corresponding Pauling bond order. In the Measurement routine these two bond orders are shown.
StruMM3D automatically detects "borderline single/double bonds" and 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. If so, then StruMM3D will designate these bond as double bonds. These "borderline" double bonds will be represented as "peach puff 3", or brown, coloured solid bonds. If you measure their lengths, StruMM3D will show you their StruMM3D and Pauling bond orders.
This is what the environmental switch/toggle "d", which cycles through "#" and "D", does when invoked manually, but now StruMM3D also intervenes and will automatically flag these borderline bonds for you. Remember that if the switch is set to "d" then no detection of "borderline single/double bonds" will occur. If it is set to "#" then StruMM3D has total discretion and automatic controll over this process. If it is set to "D" then StruMM3D is forced to always comply
Remember that StruMM3D will NOT display the energies of molecules that have missing Hydrogens, Lone Pairs, missing atoms, or atoms that are obviously erroneously sited. ALL of the valencies of ALL of the atoms must be appropriately satisfied before StruMM3D will assess a molecule's energy. Use the Main Menu > Construction routine to add Hydrogens and Lone Pairs, if you need to.
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How do I prompt StruMM3D to tidy up the file system?
If you are like me and have been reviewing the structures of many molecules from their CIFs, or just building and modifying the structures of many molecules, then sometimes you'll have structure files in places where they shouldn't be. This could be a problem, since StruMM3D automatically looks for structure files by their extensions, like xxs or sxs, unless otherwise explicity indicated by the file name.
If you run all of your molecular modeling exercises by starting StruMM3D and then loading the structure(s) you wish to examine, then StruMM3D will take care of the file system automatically. After every 10 runs, it tidies up.
However, if you have associated your files with StruMM3D, and load files by clicking on the file name in Windows Explorer, then StruMM3D does not want to interrupt the fun and does not tidy up. This could go on for a while until the file system is a mess.
Anyway, the next time you load a file by clicking on the file name in Windows Explorer, after you get back to the idle screen, and you're doing nothing, type "~ tidy 1" into the I/O Box and hit enter. If you want a really vigpous clean up then use "~ tidy 4". When you terminate, StruMM3D will tidy up for you.
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What's the best way to open a library of files?
Every now and then, especially when you are getting CIF files from the Cambridge Crystallographic Data Center (CCDC), you'll end up downloading a library of CIF files. There could be two, or many files in these libraries. It might seem that you'll have to do some work to open these libraries and to separate the files before using them, but that is not neccessary. First, save the library into the folder/directroy that you will be accessing it from.
Start StruMM3D and click on the library of files, the Str3DiFileConv utility will automatically count the number of files in the library, separate them into their individual CIFs, and convert each CIF to the StruMM3D's native XCC file format. These XCC files are much smaller than the CIF and contain all the info needed to continue the molecular modeling exercise using StruMM3D.
StruMM3D will then display the structure embedded in the library's first CIF file, from its XCC file. You can examine that structure's data and when you are done, just delete the structure in memory in preparation for examining the other files/structures from that library.
Let us assume that you had saved the library into X:\Str3Di\Imports, where X: is the drive that has the StruMM3D installation. To use the other files that were generated, use the StruMM3D main menu option Structure/Load, click on Imports, and in the text box will show X:\Str3Di\Imports\*.xcc. Click OK. All of the newly created XCC files will be presented in the file explorer window and you can the click on whichever you wish to use/view.
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Launch StruMM3D from the Molecular Grahics Thumbnails
When using StruMM3D you can save a graphic of the current image to the clipboard (there are three ways to do this within the program), and this simultaneously places that image, as a JPG or BMP file, into the current working directory. You can use this graphic in your publications/documents etc.. If you view the working folder using Windows Explorer, you can see these thumbnails (Windows makes them from the JPG or BMP file, or any other graphics file in the folder, JPG, GIF) and these thumbnails show the molecules in glorious color.
So you would now have a visual/graphic display of all the molecules that were displayed by StruMM3D!
StruMM3D allows you to right click on the thumbnail, select "open with" from the menu, direct the PC to use StruMM3D to "open" the file, and the molecular modeling of the selected structure begins. After the first run Windows adds StruMM3D to the "open with" menu and the process is easier.
You can automate the gathering of the bmp files for each structure loaded by StruMM3D by entering "~ jpgbmp 1" in the I/O Box while StruMM3D is running.
JPG files are now the default. You can make BMP files the default by entering "~ img 1" in the I/O Box while StruMM3D is running.
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What would the Pauling Bond Order be?
Pauling bond orders compare the length of any given type of bond, single, double triple, with the length of the simplest "saturated" single bond that can be formed between the two atoms. It does not take into account the hybridization states, and consequent covalent radii differences, of the atoms in the bond being examined, nor the influences of inductive effects, steric effects, and others. It is a real revelation to see what the Pauling bond order would be if it did accommodate some of these variables.
StruMM3D compares the length of the bond being examined with the simpleset analogous bond. So Single bonds are compared to single bonds and triple bonds are compared to triple bonds, a delocalized bond to a delocalized bond, and NOT to single bonds the way the Pauling calculation does. The results are much more meaningful and are much better indicators of the relative length of the bond being examined to a standard.
So, whenever you are measuring bond lengths, StruMM3D will show the "StruMM3D" bond order values so that you can compare them with the "old" values that you can compute from the bond length shown, using the obviously outdated, original, Pauling equation. Very often the StruMM3D bond order values are quite close to the Pauling values.
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A Special Note on Mn, Fe and Co Complexes
The transition metals manganese, iron, cobalt and nickel can form complexes that have the metals ions in high spin or low spin states. For each metal, these spin states are experimentally observable and can be differentiated from each other by a variety of spectroscopic methods.
As of version 220.127.116.11, StruMM3D testing algorithms to enable it to automatically differentiate between high and low spin states, largely to enable it to embrace the generality of the chemistry of the transition metals, rather than that of a few. It is widely known that the basic criterion for the differentiation of the spin states of these metals seems to be the nature/type of ligands that compose the ligand fields of these ions. In practice, the classification of ligands in this context is quite loose, and having a mixed set of ligands can greatly confuse matters. Algorithms are being tested to enable this aspect of molecular recognition in these metal complexes. There are no reliable data, as yet, for the covalent radii of Nickel in its high/low spin states.
StruMM3D now has the capability to differentiate between some of the high/low spin states of these metals in their complexes. However, care must always be used, nothing is perfect.
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Best Folder to use for Examining Imported CIF/PDB Files and Libraries
By now most of us would have come to realize that CIF and PDB files are often far from perfectly constructed/written. Disordered atoms, which create havoc during structure analysis and display, are scattered throughout the relevant CIF coordinate data section, instead of being clustered towards the section's end, and labeled for easy identification. Often the coordinates recreate the asymmetric unit and not the molecule or the unit cell. Careless writers label carbon atom A as "CA" which can be confused with "Ca". Among other problems.
Every time we load a structure into memory, StruMM3D looks at its log, and if it does not find the molecule, it enters the data into the log. If the CIF/PDB coordinate data the molecules is constructed from is flawed, then you have a flawed log entry too. So you need a safe place to examine new CIF/PDB files, especially their libraries, to keep your system clean and uncluttered by junk data.
That folder is the \Str3Di\temp folder! StruMM3D treats this folder in special ways and it is the folder that prevents you from over-writing valuable StruMM3D constructed data files (.sxs) accidentally. Put the CIF, or other suspect data into \Str3Di\Temp and open the file, with StruMM3D. After "looking" at what you got from the imported file, if/when you are happy, you can copy and paste the info into the relevant project folders in \Str3Di\projects.
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Use the \Str3Di\Projects folder for storing coordinate data from Your Projects
The \Str3Di\Data and the \Str3Di\Xray folders are meant to be basic storage and backup folders. They are not meant to be used to store coordinate data from your projects. There is a special site for that, the \Str3Di\Projects folder. If you have already started to save your data into one of these storage folder, hopefully into a suitably named sub-folder, then just cut and paste the sub-folder into the \Str3Di\Projects folder. StruMM3D will be happier, and work more efficiently, if you did. Remember also that \Str3Di\Temp is a special folder that is extensively used by StruMM3D. Don't put anything there that you don't want erased.
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Mood music for StruMM3D?
Want to "hear" something interesting? Save a bit of your favourite music, as a MP3 file, with the name mood_whatever.mp3 (where whatever is your name for the music) and copy this file into the \Str3Di\waves folder. Now launch StruMM3D and enjoy the music. If the music doesn't start, or there is a problem with the sound/audio feature, then use the P environment toggle to enable or disable it (switch it on or off).
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To find out more about Str3Di's support programs jump to THE StruMM3D MOLECULAR MODELERS