This is the the Molecular Scene Generator (MSG). It is an interactive, web based front-end for the popular molecular graphics program MolScript. MSG can generate three-dimensional VRML representations of macromolecular structures, which can be viewed in a standard web browser.
MSG is one component of the MICE project at San Diego Supercomputer Center (SDSC). The scripts underlying MSG were designed as a server-side mechanism for generating molecular scenes for the MICE application, but are also accessible via this web-site, and can be used to generate scenes outside of MICE. You can generate a scene from any structure in the Protein Databank (PDB) by simply giving the accession code for the structure of interest, or you can upload a PDB file from your local disk to our server and generate a customized view of your own structure.
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To use this site you'll need a web browser which has a working VRML viewer. This can either be a helper application which starts when you generate a scene, or, more usually, a plugin module which displays the VRML directly in your web browser. You'll need to visit the website for your browser to find out how to obtain and install the VRML plugin.
The site has been tested with recent versions of Netscape using the CosmoPlayer VRML plugin. The CosmoSoftware website has apparently gone offline and it seems to be impossible to download CosmoPlayer for Windows or Macintosh at the moment. You can still get CosmoPlayer for Irix directly from SGI.
Note: There are known problems using this site with
Microsoft Internet Explorer, versions 4 and 5. It may work for
you with IE, but then again, it may not.
To view a structure in the PDB, you'll need to know the accession code for the structure. This should be a 4 digit number, which can be a mixture of numbers and letters. If you don't know the code for the molecule you want to view, you will need to search the PDB to get that code.
Once you know the code for the structure, enter it in the box
and press the “View” button. You will be presented
with an HTML form which will let you customize the scene until
you're happy with it. To view the scene, press the
“Render” button and a new web-browser window will
appear. This
page gives a brief description of the items that you can
customize on the form (you can also get to that page from the
actual form).
Before you upload structures to this server, you should bear in mind that there are no strict security measures in place to protect the privacy of your data. While every effort is made to keep users' information private, we obviously cannot guarantee security for various reasons. Firstly, transactions between your browser and our server are not secure and are, like all other insecure web transactions, susceptible to eaves-dropping. Additionally, any files which you upload are stored in plain-text in web-accessible areas. They are stored under more or less randomly generated names, but can be downloaded by anyone willing to make enough guesses.
If you are concerned about the privacy of your data, you may want to think twice about uploading a new or sensitive structure. If you have specific questions about the site and the way it operates, please feel free to mail us.
Alternatively, you may want to operate your own version of this site on a local machine or network. The MSG scripts are available for users to download and install locally. Using them you will be able to run a local version of MSG under your own web-server, even if the server does not have access to an outside network.
MSG is available as a tarball containing all the scripts, forms and documentation needed to run it on a local webserver. You can download the tar file here. Please check the files “README” and “README.install” for help and instructions on installing MSG at your site.
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