Jmol displays of 3-D structures of Biological molecules
to go to safer Jsmol version
Bad news and Good news!
Following changes to the most recent versions of this applet, you may encounter message such as:
Jmol is blocked by Java security
Certificate has been revoked.
The application will not be executed.
This has affected a large number of webpages displaying molecular images using the Jmol applet system on other websites.
There is however a chance that these JMol applet-based pages on the BioTopics.co.uk server may be unaffected, as they are running another (older) version.
I know that there are quite a lot of users still accessing these files, rather than the JSmol versions.
It appears that the more recently updated JSmol versions are unaffected .....
Please let me know if these molecules are being displayed (or not) on your system.
[Please use the feedback icon]
This section of the BioTopics website relates to Biological chemicals, allowing them to be visualised as 3-D interactive molecular images which can be explained in an interactive way.
If you opt to follow the links in the table below you are likely to be repeatedly warned about security issues. I believe there is no specific risk in the files themselves - they are not virus-infected - but accessing them via Java may open users' computers to malicious functions. These pages are all easily accessible after passing the warning page which is shown at first.
I have now produced a series of JSMOL pages as a replacement to these ones.
Here is the equivalent menu page:
Java security work-around
You can now add:
to your exception site list (cut and paste the line above).
This can be accessed from Windows control panel, search for Java, double click Java icon to get to Java control panel, then security tab and edit site list ...
Please let me know if this is successful, or if you need more assistance.
These files have been written or converted to use the Jmol Java applet (currently version 11.00 on this server), so they ought to be visible in almost all modern computers.
However Internet Explorer 6 with Windows XP (and also IE7 with or without Windows Vista) may block this functionality; images may need to be clicked on before they become movable using the mouse. Some of the control scripts may also trigger an over-cautious reaction.
Please use the feedback link on the left to let me know if these images do (or do not) display on your computer.
Most Apple desktop and laptop models use Java and should give very clear images with these files - especially the proteins on larger screen sizes.
Sadly, iPads and most tablets do not use Java, so these molecules will not display on them.
The three-dimensional, rotatable, scalable images on these pages should be fairly easily displayed using the Jmol Java applet, if you have Java enabled in your browser.
Jmol, which is open source (free), runs from the same server as these
pages and so is available to all users (effectively regardless of
It is an alternative to the Chime plug-in, which users
have to install on their own computer (not easy with educational
networks). Unlike Chime, Jmol is also being continuously developed.
Although there will be an initial delay as the applet loads, subsequent
pages should be quicker. Each link below will bring in a separate
overlay page, leaving this list page beneath it. After use, simply
close these windows in the usual way (use the icon below or click on
the X in the corner of the browser window).
||alpha and beta glucose
|storage compounds - animal
|storage compounds - plants
||amylose [another form of amylose]
|structural compounds - plants
|| amylose-iodide complex
|All shown on one page
||20 amino acids
|Individual amino acids
- seen a little larger
|Levels of protein structure
||as shown by Insulin
|as shown by Haemoglobin
||as shown by Myoglobin
Amylase as an example
|More to be added soon|
|LIPIDS (FATS and OILS)
|| saturated and unsaturated fatty acids
|Polyunsaturated fatty acids
|More about functional foods
plant sterols and stanols and their esters
|| monoglycerides and diglycerides
|| phospholipid bilayer
|Sterols and steroids
|| More to follow
||DNA - see also * below
||NAD and reduced NAD
|Other molecules of biological interest
||Another fungal product
|| Anti-Tuberculosis Drugs
||Opiates and cannabinoids
||Salicin and Aspirin
[missed out - a number of images of vitamins]
I am very grateful to the (largely unknown) people who provided the original data files for these molecules, mostly in
.mol , .pdb and .xyz format.
However not all of the representations of molecules on the internet are completely reliable, so beware.
I have recently started producing my own co-ordinate files (or modified/corrected versions of other people's files!) using ACD ChemSketch
And the I find the Jmol application modelkit
very helpful in modifying and fine-tuning molecular structures. Several files here need this treatment.
You can access lots of information from the
RSCB Protein Data Bank which "provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease". It has a very readable section Molecule of the Month - Alphabetical List which gives background information about Biochemical molecules without going overboard with (much) excessive detail or heavy graphics.
European Bioinformatics Institute is an Outstation of the European Molecular Biology Laboratory and provides access to all sorts of information about biological molecules.
The DrugBank database is a unique bioinformatics and cheminformatics resource which I have found quite useful.
ChemSpider is a free chemical structure database owned by the Royal Society of Chemistry.
RASMOL is a stand-alone 3D viewer for molecules using these formats,
effectively an application on which Chime, Protein Explorer and Jmol
*RasMol for RISC OS
There is also a stand-alone application version of Jmol which is also
available for development work, independent of web page format. This is especially good in full screen mode.
Jmol-based molecular visualisation files on other web sites
Jmol is looked after by a very enthusiatic (worldwide) team of practitioners:
I am extremely grateful to Eric Martz,
Professor Emeritus, University of Massachusetts, who advised me to concentrate on the use of Jmol for molecular display on these web pages rather than waste time with Chime. His current interest is "Macromolecular Visualization and Structural Bioinformatics"! and is involved in FirstGlance in Jmol and Protein Explorer, both of which are used in exploration of protein structure.
My sincere thanks also go to Bob Hanson, Professor of Chemistry at St. Olaf College Northfield, MN, USA, who maintains and extends Jmol -see the Jmol development page. He appears to fix bugs as fast as they are discovered, and add new features at an impressive pace. Here is a very useful molecule viewer he has put together.
(Webmasters only: Jmol can be downoaded here:
Dr Angel Herráez, Univ. de Alcalá (Spain) is another enthusiastic user of Jmol (he has just produced a book to explain its use - more details later).
He maintains some very useful resources such as:
*DNA structure a modified version of an excellent Chime-based tutorial
*Molecular Models for secondary education an impressive tutorial translated from Spanish
Both can be accessed from an index page at
Dr Frieda Reichsman has also produced an excellent range of molecular animations visible online at http://www.moleculesinmotion.com/
is a collaborative, 3D encyclopedia of proteins and other molecules. Eric Martz says "Proteopedia will develop into one of the most useful on-line reference sites for
structural information about macromolecules. Proteopedia already
contains an automatically-generated page for each of the nearly
50,000 entries in the Protein Data Bank. This automatic page contains
the molecule in Jmol, with green links to display every site and
ligand in the PDB file (echoing their full names), the abstract of
the paper, and links to a few other particularly useful structure
services and resources.
Students and Educators can develop macromolecular structure tutorials
in Proteopedia far more easily than in any other system at present."
Orientations of Proteins in Membranes (OPM) database
OPM provides spatial arrangements of membrane proteins with respect to the hydrocarbon core of the lipid bilayer.
This is quite a comprehensive selection of important biological molecules, visualised as a sandwich between two discs of red and blue dots, showing how these proteins interact with membranes on the surface of, or within, the cell.
Please let me know of any other Jmol based information sources at an appropriate level.