Some Updating Things For StruMM3D Users to do ASAP!

We strongly suggest that users only launch StruMM3D using StruMM3DX.Bat in order to facilitate future automatic updating processes that will occur occasionally. If you do not use StruMM3DX.Bat, then manually update StruMM3D from the download StruMM3DUpd.Exe file, that is available on this page.

The covalent radius database for metals used by StruMM3D is now being re-examined and refreshed. Important changes are being made. This file along with any other newly updated helper files for StruMM3D can be obtained from this StruMM3DUpd.Exe download.

StruMM3DUpd.Exe is a 7zip self-extracting archive of recently updated StruMM3D files. Save it to the folder \Str3Di and click it, accept all the overwrites.

No Internet? or Don't Want StruMM3D to Access the Internet?

The document StruMM3DComLine.Dat has a listing of most of the programme's "paramenter switches", it is well worth reading. You should implement these parameter changes very sparingly and carefully. Only make changes that are really necessary, including the one to block the programme from seeking internet access. However, if you don't have access to the internet and/or face slow starts, just add "~ nowww 0", without the quotation symbols, to the last line of StruMM3DComLine.Dat.

An Important StruMM3D Milestone!

The Quantized Valence Bond Molecular Mechanics (QVBMM) force field is founded on the notion that all bond types are quantized, and that the length of any bond must be indicative of it's quantized bond type and hence bond order. StruMM3D uses this force field, and has facilitated the reviewing of the bond type/bond length data for tens of thousands of x-ray crystallographically determined structures, organic, organometallic and inorganic.

35 Years after the creation of the QVBMM force field, for every high resolution diffraction determined structure (excluding those with disordered atoms) examined using StruMM3D, there has never been one case of a violation of the quantized bond type/bond length idea. For 35 years StruMM3D has verified that the quantized bond type/bond length notion has been upheld.

StruMM3D Update News

If you seem to be missing a copy of the file MSCOMCTL.OCX from your system, then there is a copy in the updating file StruMM3DUpd.Exe, whose download link is below. Remember that MSCOMCTL.OCX must be placed in C:\Windows\SysWOW64.

Remember to visit the StruMM3D FAQ for hints, user/programme tips, and additional help. The FAQ is updated frequently and always has new interesting information.

Some users just don't take the time to change the names of their molecular models after they have modified their structures. This brings chaos to the saving of the coordinate data for molecular models. We are trying to make the process more friendly, especially if the StruMM3D environmental parameter "T" (autosave temporary structure data files on structure change) is set.

If you make any change to the model in a working folder, to prevent the overwriting of old data immediately, it will be automatically saved into \Str3Di\Temp, with an included _temp designation. These files temp are useable, can be renamed, and re-saved (but remove the 'temp' designation) into other folders. StruMM3D does not save any file with "_temp" in its name to any other folder than \Str3Di\Temp.

The release of the version 9.0.0.1, of StruMM3D, marked the move towards a more graphical usage of StruMM3D. This, and subsequent, version will dramatically reduce file storage space used, if we remember that the folders \Str3Di\data and \Str3Di\xray are storage/backup folder and should not be used as working folders. Users should create appropriately named folders in \Str3Di\projects for their projects and these folders will enjoy full access to the new graphical features.

StruMM3D maintains a comprehensive database of molecules that have been viewed/examined/manipulated. StruMM3D must examine this database periodically to keep it up to date, verify the validity of the entries, and remove deleted molecules. This is all done when you log off, or exit from the program, but in the background, allowing you to do something else with your computer and time. So, we ask you to give StruMM3D a few minutes to complete it's chores, especially if you have a large database of molecules.

StruMM3D normally measures molecular (steric, torsional, dipolar) strain energy. Algorithms that link bond orders (and bond lengths) to the efficiency of delocalization in simple conjugated pi-systems, while present in StruMM3D's code, had not previously been made available to the user. It has been the foremost belief that if molecular strain can adequately reflect, and account for, molecular stability and reactivity, then this would minimize the instances in which quantum chemical assumptions need to be used, and so force users to face the reality that much of quantum chemistry has only very narrow and specific applications.

Indeed, over the years it has been demonstrated that many complex stereo-electronic phenomena in organic chemistry, like the anomeric effects, can be explicitly and completely explained by looking at molecular stereo-electronic strain energy rather than by invoking obscure and specious implementations of delocalization theory promoted by some quantum chemistry calculations.

We have developed algorithms for predicting the best covalent radius size for metal ions in their complexes. This is an extremely important area because the use of inappropriate covalent radii has lead to researchers claiming the existence of metal to metal triple and quadruple bonds, where none actually exist. Many of these debacles are instigated by quantum chemists. Usually, in normal chemistry, the greater the order of a bond, the shorter it is. However in quantum chemistry, quadruple bonds can have the same lengths as double bonds and maybe even single bonds, or longer. Go figure!

Indeed, when one adjusts the covalent radius of the metal atom, interactively from oxidation state 0 to whatever, often very surprising structural and stereo-electronic features of the complex become apparent, especially in the metal to metal and metal to ligand bonding features. When more than one viable covalent radius choice is possible, one can often see why one is preferred by looking at the metal to ligand bonding features. It is very instructive to look at the structures of metal complexes with the CCDC's Mercury and then with StruMM3D. The complexity of this field is still apparent. We have continued to refine our this metal ion covalent radius algorithm and the most recent update, embedded in the StruMM3D versions 8.4.0.66 and later, have performed very well.

StruMM3D was originally designed to be a teaching tool for undergraduate/graduate use. So, when StruMM3D is executed by a new user it will run in its "novice" mode (the moreinfo environmental flag will be M). StruMM3D is packed with neat features, and so it is highly recommended that a new user tolerate the additional information hints (a few extra click of the mouse) until one's familiarity with StruMM3D has grown. When desired, these information prompts can be dispensed with (main menu-utilities-program parameters click on M).

Remember that StruMM3D will create shortcuts to StruMM3D.Exe and StruMM3DX.Bat on your desktop from the Main Menu, HELP option. Use the StruMM3DX shortcut routinely since it minimizes the intrusion of the Microsoft UAC annoyance.

Increasingly we have seen the Microsoft security protocols preventing the Str3Di programs from running as they should. This is a permissions problem that affects even some of Microsoft's older non-system software, like when you try to open a command prompt. We advise all users of StruMM3D to use Windows File Explorer to open the \Str3Di folder, to right click on the StruMM3D.Exe file, select properties, then select Compatibilty, and then to check the box that says "Run this program as an administrator". Repeat this sequence for all of the Str3Di Exe files whose names start with "str".

Users of Windows Vista/7/8/8.1/10, will already have the required DLLs in their C:\Windows\System32 folder. Most computers will already have these DLLs in C:\WINDOWS\SYSTEM, C:\WINDOWS\SYSTEM32, or C:\WINNT\SYSTEM32. However, if you have the Windows Vista OS, or when you try to run StruMM3D you get an error message about a missing DLL, then download this VBRUN60SP6.EXE, copy it to your SYSTEM32 folder (see above) and unzip the file there. If you are only missing VB6 run-time files, these are available in the run-time library for VB6, vbrun60sp6.exe. Just download it and run/open it.

Click VBRUN60SP6.EXE to download the run-time files for VB6 (about 1005 K). Once you have the file, just click on it and the VB6 run-time files will be installed into your computer. Users of Windows 7 or 8 should right click on the executable (EXE) file, select properties, select compatibility, and then select “Run this program as an Administrator”.

StruMM3D needs a file named STRLOGO.LXS, for its proper functioning. If there is a crash during the first execution of StruMMD it could be because the critically important file STRLOGO.LXS was not found in the folder \Str3Di. There is a copy of this file in the folder \Str3Di\Data and so you can use Windows Explorer to copy the file into the \Str3Di folder. Also put a copy into \str3Di\Backup while you're at it.

StruMM3D also needs a file named Str3DiDrive.Dat, for its proper functioning. This file is included in all installation packages, and should have been installed into Drive C:\ProgramData\Str3Di after your first use of StruMM3D. If your installation tells you that it is missing, look for a duplicate in the installation folder, X:\Str3Di where the program is installed. If this file is missing from X:\Str3Di then you can get a copy from StruMM3DUpd.Exe, above, and place it in X:\Str3Di. Follow the instructions described above (New Users).

Launch StruMM3D from the Molecular Grahics Thumbnails

When using StruMM3D, it automatically saves a graphic of the molecule you just loaded, into the current working directory, unless you forbid it. You can also 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 and into the directory \Str3Di\Graphics, overwriting the older images of the same molecule. You can use this graphic in your publications/documents etc.. If you view the folder using Windows Explorer, you can see these thumbnails (Windows makes them from the BMP, GIF, or JPG file) and these thumbnails show the molecules in glorious detail and color.

So, if you so you wished, you could have a totally visual/graphic display, in Windows Explorer, of all the molecules processed by StruMM3D!

If image capturing is somehow disabled, all you need to do is to enter the command "~ jpgbmp 1" into the Data I/O Box when StruMM3D is idle, once. The process can be discontinued by entering "~ jpgbmp 0" into the I/O Box when StruMM3D is idle, and remember to omit the quotations.

StruMM3D now captures images as JPG files, the default. If you want BMP files then enter the command "~ img 1" into the Data I/O Box when StruMM3D is idle, or add this command to the end of the file StruMM3DComLine.Dat. The command "~ img 0" makes JPG files the default again. As of Version 8.2.0.10, if you right click on a thumbnail, select "open with" from the menu, and direct the PC to use StruMM3D, then the molecular modeling of the selected structure will begin. After the first run the process is easier. In older versions of StruMM3D, the graphics file must be in the same folder as the stucture data file.

StruMM3D, from version 8.2.0.10, has now become the first totally graphical molecular modeling tool, and one needs not try to remember which structure data file name corresponds to which structure. You can see them.

Remember that StruMM3D only backs up all the graphics files into the directory \Str3Di\Graphics, as well as into the directory with the structure data files. So, if you have been using data from the directory \Str3Di\Data, the thumbnails will also be saved there (automatically), as JPG or BMP files, and that is where best to use Windows Explorer to view and select the thumbnail you want to use to start a molecular modeling exercise.

StruMM3D will use any graphics file in the formats BMP, JPG, or GIF, but it can only create JPG and BMP files. Having a lot of high resolution BMP files on your drive takes up a lot of space, but you can convert them to smaller JPG or GIF files since StruMM3D will also use these files. We recommend using the open source program "Magick" in the ImageMagick Software package to convert your BMP files to JPG files. If you want StruMM3D to facilitate this conversion for you, using ImageMagick's Magick or Convert, write to us and we'll show you how.

So, you are searching for a molecular structure using Microsoft File Explorer, would you rather see -

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If you have any trouble, with the installation, or the software, just send us an e-mail, to customer support, so that we can assist you.

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