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


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


STR3DI TEMPLATES for MOLECULAR MODELING and MOLECULAR GRAPHICS.

Using suitable template structures, you can assemble the most complex molecules easily and efficiently using StruMM3D. Often the problem is finding a suitable template structure. We will try to supply you with these, on request, and will often post them on this page if enough users ask for these structures.

Click here to get the updated file with The Basic Set of Template Structures that are packaged with the STR3DI molecular Modelers. We also provide you with a set of amino-acid structures (in this zipped file), for use as templates.

The structure data files listed below were actually placed here to demonstrate the ability of StruMM3D to perform as a "helper" application, or “plug-in”, with the Microsoft Internet Explorer 11 web browsers.

The molecular models embedded in these structure data files will also start you out on your molecular modeling experience at your home/classroom/lab/workplace.

Normally, provided that you have associated the SXS, XCC, XLC and XXS file extensions with StruMM3D, if you left-click on one of the structure URLs below the browser should download the file into the “Temporary Internet Files” folder, and then execute StruMM3D and use it to open the structure file you clicked on.

The Mozilla FireFox browser, as of version 3.6.13, it does “read” file associations from your computer’s operating system, registry. So, if you are using Mozilla FireFox, when you left-click on a data file it will import the structure into StruMM3D and a full molecular modeling experience can be enjoyed.

If you have associated the STR3DI extensions, and you still get an error when you left-click on any URL below, then you have a small problem of a missing key in your system’s Registry. When you had associated the file extensions .sxs and .xxs with StruMM3D, the computer should have created these Registry Keys. It might be that the system did not do so, or later erased them. We can supply you with the Registry Keys that will enable your computer to become fully compatible with StruMM3D’s files.

If the file does not open to display the structure in StruMM3D, then StruMM3D users (that now have FileConv) can download the selected file to their \Str3Di\Imports folder (use the mouse right-click and save as), and then click on the file to display the structure.

If you wish to use StruMM3D in online molecular modeling exercises, then we have to recommend that you use the Mozilla FireFox, version 3.6.13, or newer, web browser. If you have an older version of FireFox, then use Microsoft’s Internet Explorer 11, or newer, or Microsoft Edge..


Some Simple Acyclic Alkanes

propane
anti-butane
gauche-butane

Some Simple Cycloalkanes

Cyclopropane
Cyclobutane
Cyclopentane
Cyclohexane
Cycloheptane
axial methylcyclohexane
equatorial methylcyclohexane
trans-decalin
cis-decalin
trans-hydrindane
cis-hydrindane

Some Heterocycles

cis-1,8-dioxadecalin
trans-1,8-dioxadecalin
pyridine
pyrrolidine
a quinoline
tetrahydrofuran
tetrahydropyran
Thiophene
Thiopyran

Some Natural Products and Their Derivatives

an iridoid natural product
gibberellic acid methyl ester
the germacranolide sesquiterpene hallerin
a cyclodextrin
a pair of derivatized bucky balls
papulacandin (drawn using STR3DI)

Some Biologically Important Synthetics

aspartame

Many more templates are available. Tell us which structures you want to model and we'll supply these. Remember that you can also get atomic coordinate data in other formats and convert these to STR3DI format using our FILECONV utility.


To find out more about STR3DI's support programs go to THE STR3DI MOLECULAR MODELERS.