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Using StruMM3D to look along the axis of a DNA double helix fragment
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Have you StruMM3D a molecule today?
We pronounce StruMM3D like “strumm 3D”, or, better still, “strummed”. Indeed, we use it to reveal, display, and examine, the sweet molecular music that nature plays, and the currently available version is the best ever.
Recently StruMM3D has been rated as - “Awesome, easily the best molecule viewer/modeler of all time. The information StruMM3D mines from diffraction (XYZ) data, and molecular models, is most impressive.”
The recently published, and excellent, work of Ingo Krossing et al., (Science 2013, DOI: 10.1126/science.1238849), on the x-ray structure of the 2-norbornyl cation has enabled us to update the QVBMM force field, and so to make StruMM3D version 22.214.171.124 the first, ever, molecular mechanics program that can examine every aspect of a transition state structure. Organic chemists will be delighted by these new features in StruMM3D, especially since the transition state model can be systematically modified to reveal energy trends.
Indeed, StruMM3D can now, automatically, identify transition state bonds in x-ray crystallographic determined structures, no human-generated connectivity tables needed, a boon to molecular voyeurs and crystallographers alike.
From the release of version 126.96.36.199, users will enjoy the full capabilities of our prized data file conversion utility FILECONV, for zip, nada, free. So go ahead, just launch StruMM3D, load any file of coordinate data, from most molecular modeling suites (CSD, PDF, CIF, XYZ, MOL, etc.), and you'll have a structure to examine. Unless, of course, the targeted data file has flaws, which is common because they are so complex, unlike StruMM3D's files.
The release of version 188.8.131.52 marks the successful attainment of one major step in StruMM3D's quest to finding global molecular energy minima, and new code for calculating bond orders. Version 184.108.40.206 has a re-worked algorithm for the automatic detection of functional groups, better program stability, and more conservative memory/energy usage.
The release of StruMM3D version 220.127.116.11 will mark an important milestone. This version sports a new colour scheme for atoms, which carries more structural stereo-electronic information. Re-designed working windows, more crash-proofing protection (from bad data and ill-advised user input), and faster graphics round out the list of obvious improvements. There are others too, but we can't elaborate here. StruMM3D is really ready to reggae now.
Hmmmm, we wonder what StruMM3D's users will think now.
The rational starting point in the molecular modeling of any organic molecule ought be the process of ascertaining how well the known (experimentally determined) properties of that molecule (physical and chemical) can be simulated by considering only its the bond length, bond angle, and dipolar features. These simulations are best done with molecular mechanics (MM) programs.
In order to truly UNDERSTAND the real roles of these dipolar data, your molecular modeling program MUST allow you to examine all of the molecule's potential energy data. Indeed, these data, for each, and every bond, bond angle, and lone pair interaction, can give invaluable insight into the most subtle and important features of the molecule. Most QM programs, and many MM programs, CANNOT give you this data, and so you will have NO idea how the modeler arrived at its energy distribution. However, StruMM3D does give the molecular dipolar and other strain data, routinely, without special effort.
It is only if an initial simulation of the dipolar features of any molecule proves to be inadequate, that one can truly begin to understand the contributions that are being made to the molecule’s structure, and properties, by delocalization and quantum mechanical (QM) effects. This notion is especially important since it is well known that QM programs cannot reliably simulate lone pair repulsions, and offer poor simulations of dipolar effects in general, unless another multitude of assumptions are made.
Regardless of the hype that is bandied about by users of QM programs, many of whom have no idea how these programs are designed, the reality is that QM calculations are far from being “ab initio”. Indeed, since it is impossible to generate an exact solution to the wave equation of the helium atom, and any possible solution requires a host of approximations, then imagine the multitude of approximations needed for solving the wave equation for methanol “ab initio”.
Is it then surprising that most QM investigations begin with MM generated molecular models?
Incidentally, if you regularly review structures that have been determined by the diffraction methods (x-ray crystallography etc.), then you simply MUST use StruMM3D to visualize your data. StruMM3D is the ONLY molecular modeler that enables you to spot weird bond lengths, among other oddities, that find their way into diffraction studies. Serious crystallographers always use StruMM3D.
The QVBMM Force Field
StruMM3D is powered by the most sophisticated molecular mechanics force field ever developed. The QVBMM force field. StruMM3D’s advanced structure recognition and analysis algorithms enable the user to input molecular structure data by using only atom types and atomic coordinates. These algorithms ensure that faulty user-generated atom connectivity list never introduce structural errors into the molecular modeling exercise.
The newly re-parametrized QVBMM force field, first released in version 7.1.0.X of StruMM3D, has wildly surpassed our expectations. These new algorithms have performed flawlessly. We shall continue to drive the programme closer to perfection because of the important role that MM calculations play in real science.
As mentioned above, the recently published x-ray structure of the 2-norbornyl cation, has allowed us to complete and validate the QVBMM algorithm that handles transition states and single bonds with bond orders less than 0.5. StruMM3D now becomes the first molecular mechanics program to successfully handle transition states.
Update Your StruMM3D.Exe
Remember to visit the StruMM3D FAQ for hints, user/program tips and additional help. StruMM3D also tells you when a newer version is available so that you can get it. However, if you haven't updated your StruMM3D recently, go download and try the newest version of StruMM3D. It is faster and is just awesome! The docking animation is quite nice!
Users of versions of Str3Di32 must update to StruMM3D, which has total backward compatibility with all Str3Di structure files.
Current users of StruMM3D should download only StruMM3D.ZIP and unzip it into their Str3Di folder/directory, to apply recent minor updates.
If you're not using StruMM3D.EXE, then why not?
Do you want to see how good your current molecular modeling program is? Or isn’t. Then we dare users of other molecular modelers to see how quickly they can complete one of our very routinely done molecular modeling tasks. This one involves using your current molecular modeling program to spot flaws in the coordinate data of published x-ray crystallographic investigations. Try it.
StruMM3D is compiled with VB6 and so has an EXE that is faster, smaller, and totally compatible with Windows 7 and Windows Vista. Any User Account Control issues that you might have had in the past should no longer occur. You should not need to execute StruMM3D by using the “run as an administrator” option. However, if StruMM3D does not start the first time, just right click on the file, StruMM3D.Exe in the directory/folder \Str3Di, and select “Run as an Administrator”.
For more information about our services and products - Write to us
Visit our Exorga's Web Goodies site for some links a variety of websites that we have found to be both interesting and entertaining. You will be delighted by these sites.
Visit our Exorga's DOWNLOADABLES site for access to StruMM3D, and to some utilities we have found to be very useful.
We offer unsurpassable, confidential consultation in organic chemistry, environmental chemistry, molecular modeling, and in the development of custom chemistry software. We can provide you with expert advice in the construction of molecular databases, and in the conversion of your industrial organic chemical by-products into valuable materials.
Via US Mail at - EXORGA,INC., P. O. Box 56, Colonia, New Jersey 07067, U.S.A.
Via e-mail at - Exorga, Inc. E-mail.
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Last updated – 03-03-2014