ChimeTM and Chime ProTM Frequently Asked Questions

Installation and Configuration: Using Chime:
Developing Pages with Chime: Troubleshooting:

Installation and Configuration

What is the current version of Chime and Chime Pro and what platforms are supported?

Chime Pro is currently at Version 2.0 Beta 2 for Windows 95 and NT, and Version 1.01 for Windows 3.1, and PowerPC plus 680x0 Macintoshes. Chime Pro is currently at Version 0.9e for the SGI.

Chime is currently at Version 2.0 Beta 2 for Windows 95 and Windows NT, and Version 1.0 for Windows 3.1, PowerPC Macintosh and 680x0 Macintosh. Chime Pro is currently at Version 0.9e for the SGI.

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What gets installed on my machine by the Chime / Chime Pro 2.0 Installer?

For Windows 95 and NT the installer does the following:

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What is easiest way to check that Chime / Chime Pro is installed correctly on my workstation?

If you have installed Chime / Chime Pro correctly you will see an entry for it and a list of the mime types it supports when you select the menu item "Plug-ins" from the "Help" menu in Netscape Navigator (the Help button on the Macintosh is a question mark icon.)

For Internet Explorer there is no "Plug-ins" menu item available. You will have to try one of the demonstration pages to see that Chime / Chime Pro is installed properly.

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What should I see if Chime / Chime Pro is installed properly?

If you have installed Chime / Chime Pro properly you should see a spinning bucky ball in a black box immediately below this sentence:

If not, you will see an empty box directly above.

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How do I make my server understand the various chemical mime types?

Your web browser decides which plug-in (or helper application) to use for a Web browser link or embedded plug-in based on the "mime-type" or specialized data encoding. Local files on your workstation are assigned a mime-type based on their extension. Files on a server, however, must be tagged by the server so that your web browser can recognize the mime-type. This is done through a designated configuration file on the server. Otherwise, your web browser will display a "broken plug-in" icon or may load a previously requested helper application for your chemical structures.

If you are using Netscape Server your server administrator must add the following lines to the mime.types configuration file: 

   type=chemical/x-mdl-molfile          exts=mol
   type=chemical/x-mdl-tgf              exts=tgf,skc
   type=chemical/x-mdl-rxnfile          exts=rxn
   type=chemical/x-pdb                  exts=pdb,emb,embl
   type=chemical/x-gaussian-cube        exts=cub,cube
   type=chemical/x-gaussian-input       exts=gau
   type=chemical/x-xyz                  exts=xyz
   type=chemical/x-mopac-input          exts=mop
   type=chemical/x-csml                 exts=csm,csml
   type=chemical/x-jcamp-dx             exts=jdx,dx
   type=application/x-spt               exts=spt
   type=application/x-rasmol            exts=scr
   type=application/x-javascript        exts=js

You must restart your server for these changes to take effect.

For Cern HTTPD your server administrator must add the following entries to the httpd.conf file: 

   AddType .mol   chemical/x-mdl-molfile        8bit    1.0
   AddType .tgf   chemical/x-mdl-tgf            8bit    1.0
   AddType .skc   chemical/x-mdl-tgf            8bit    1.0
   AddType .rxn   chemical/x-mdl-rxn            8bit    1.0
   AddType .pdb   chemical/x-pdb                8bit    1.0
   AddType .emb   chemical/x-pdb                8bit    1.0
   AddType .embl  chemical/x-pdb                8bit    1.0
   AddType .cub   chemical/x-gaussian-cube      8bit    1.0
   AddType .cube  chemical/x-gaussian-cube      8bit    1.0
   AddType .gau   chemical/x-gaussian-input     8bit    1.0
   AddType .xyz   chemical/x-xyz                8bit    1.0
   AddType .mop   chemical/x-mopac-input        8bit    1.0
   AddType .csm   chemical/x-csml               8bit    1.0
   AddType .csml  chemical/x-csml               8bit    1.0
   AddType .jdx   chemical/x-jcamp-dx           8bit    1.0
   AddType .spt   application/x-spt             8bit    1.0
   AddType .scr   application/x-rasmol          8bit    1.0
   AddType .js    application/x-javascript      8bit    1.0

You must restart your server for these changes to take effect.

For NCSA HTTPD or Apache your server administrator must add the following entries to your server configuration file: 

   addtype chemical/x-mdl-molfile        mol
   addtype chemical/x-mdl-tgf            tgf skc
   addtype chemical/x-mdl-rxnfile        rxn
   addtype chemical/x-pdb                pdb emb embl
   addtype chemical/x-gaussian-cube      cub cube
   addtype chemical/x-gaussian-input     gau
   addtype chemical/x-xyz                xyz
   addtype chemical/x-mopac-input        mop
   addtype chemical/x-csml               csm csml
   addtype chemical/x-jcamp-dx           jdx dx
   addtype application/x-spt             spt
   addtype application/x-rasmol          scr
   addtype application/x-javascript      js

You must restart your server for these changes to take effect.

For Microsoft Internet Information Server, add the following to the HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\Inetinfo\Parameters\MimeMap section of the registry file: 

   chemical/x-mdl-molfile,mol,,5
   chemical/x-mdl-tgf,tgf,,5
   chemical/x-mdl-tgf,,skc
   chemical/x-mdl-rxnfile,rxn,,5
   chemical/x-pdb,pdb,,5
   chemical/x-pdb,,emb
   chemical/x-pdb,,embl
   chemical/x-gaussian-cube,cub,,5
   chemical/x-gaussian-cube,,cube
   chemical/x-gaussian-input,gau,,5
   chemical/x-xyz,xyz,,5
   chemical/x-mopac-input,mop,,5
   chemical/x-csml,csm,,5
   chemical/x-csml,,csml
   chemical/x-jcamp-dx,jdx,,5
   chemical/x-jcamp-dx,,dx
   application/x-spt,spt,,5
   application/x-rasmol,scr,,5
   application/x-javascript,js,,5

For other HTTP servers see your administration documentation.

Note: JavaScript files (.js) are not directly used by Chime but can be used as part of applications which use JavaScript to manipulate Chime.

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Using Chime

What are the different file formats that Chime understands?

Chime understands the following input formats:

Input File Type Mime Type File
Extension		 Version First
Supported
MDL Molfile chemical/x-mdl-molfile .mol 0.8
MDL Transportable Graphics File chemical/x-mdl-tgf .tgf 2.0
MDL Sketch File (platform specific) chemical/x-mdl-tgf .skc 2.0
MDL RxnFile chemical/x-mdl-rxnfile .rxn 1.0
Brookhaven Protein Databank chemical/x-pdb .pdb 0.8
IEMBL Nucleotide Format chemical/x-pdb .emb,.embl 0.8
Gaussian Cube File chemical/x-gaussian-cube .cub,.cube 0.8
Gaussian Input File chemical/x-gaussian-input .gau 0.8
Minnesota Supercomputer Center's XMol XYZ chemical/x-xyz .xyz 0.8
Mopac Input File chemical/x-mopac-input .mop 0.8
Chemical Structure Markup Language File chemical/x-csml .csm,.csml 0.8
JCAMP-DX File chemical/x-jcamp-dx .jdx,.dx 2.0
Rasmol Script File application/x-spt .spt 0.8
Rasmol Script File application/x-rasmol .scr 2.0

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How can the user manipulate Chime?

The Chime plug-in is live on the HTML page and can be manipulated:

Additional information is also available on Eric Martz's Chime pages.

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Chime doesn't currently support the chemical mime type XXX. When will it?

We are very interested in supporting (in conjunction with the Chemical Mime Community) all relevant chemical mime types. If you wish to add a new format please see the Mechanism for proposing new types on the Chemical MIME Home Page. In addition, you may wish contact us at chime-feedback@mdli.com. Support for additional mime types approved by the Chemical Mime Community becomes much easier if we are provided with appropriate source code for parsing the input file.

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How do I get the structure in the Chime plug-in into ISIS/Draw?

Chime 1.0 supports a hot-link to ISIS/Draw 2.1 which is currently available for Windows and should be available for the Macintosh and SGI in 1998. You can "hot-link" the structure in the chime plug-in by using the "Edit" "Transfer to ISIS/Draw" menu in Chime.

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Chime is great, but I want to search and retrieve structures from an ISIS database.

MDL officially announced Chemscape Chime ProTM and Chemscape ServerTM at the MDL UK User's Group Meeting on March 11, 1996. They were demonstrated at the MDL US User's Group Meeting in Philadelphia on May 9, 1996. Chime Pro and Chemscape Server provide full access to ISIS/Host databases including molecule, reaction and Oracle databases. as well as full structure searching capabilities. MDL delivered Chime Pro 1.0 and Chemscape Server 1.0 on September 30, 1996. More details are available on our Chemscape Chime Pro and Chemscape Server page.

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Developing Pages with Chime

How do I embed a Chime plug-in into an HTML page?

By using the EMBED tag in an HTML document you can insert a plug-in into a Web browser page. The basic format of the EMBED statement is: 

   <embed src="{source url}" height={hvalue} width={wvalue}>

   where:

      {source url} - input file to the Chime plugin.
      {hvalue}     - height of the plug-in on the page, usually in pixels.
      {wvalue}     - width of the plug-in on the page, usually in pixels.

For example: 

   <embed src="chim0006.mol" width=200 height=150>
renders an MDL Molfile within an HTML page with dimensions of 200x150 pixels. For more information on the EMBED tag and its options, see Embed Tag Options Reference.

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What are the specific EMBED options allowed by the Chime plug-in?

See the Embed Tag Options Reference.

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How many Chime plug-ins can I have on one page?

It depends. Later versions of Netscape Navigator are much better at handling multiple plug-ins on one HTML page. With Netscape Navigator 3.0 and later we have been able to display more than 60 plug-ins on one page coming from separate connection table files. With our new "in line" capability, where data for the plug-in comes directly from the HTML page, we have successfully loaded 300 2D molfiles on a single page. The biggest limitation is Memory. Although the code for the Chime plug-in is only loaded once each structure connection table must be loaded into memory separately. Therefore, you may run out of memory if you try to load too many plug-ins on a machine with inadequate resources. Note that Netscape Navigator uses SmartHeap for memory management and is better at handling multiple plug-ins than Internet Explorer. If you are displaying many structures you should split them between several HTML pages (via the standard "paging" mechanism that many HTML applications use.) Note that starting several plug-ins with rotating molecules will severely degrade rotation performance.

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How can I make it faster for users to access large structures on my Web site?

Chime supports compression of structure files using the GZip (GNU Zip) method. There are versions of the GZip program available for Mac, Windows and Unix platforms. To use GZip, first process the file, then make sure it has its original name. For example: $ gzip myfile.pdb

This will create a file named 'myfile.pdb.gz' on a Unix server. It must be renamed for Netscape Server to recognize its mime type properly:

$ mv myfile.pdb.gz myfile.pdb

Be careful when you transfer GZip'ed files via a program like ftp. GZip files are binary; if you transfer them in ASCII mode they will be corrupted and you are likely to see very strange results in Chime.

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How can I specify colors for individual atoms or atom types in a molecule?

To specify colors for individual atoms, include the following line within your EMBED tag:

script="select atomno=1; color atoms red; select atomnno=2; color=blue...; select *"

To specify colors for atom types, include the following within your <embed> tag:

script="select *.c; color atoms black; select *.h; color=red...; select *"

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How can I put buttons in my HTML document that manipulate structures in a Chime window?

Chime supports two scripting formats that can be used to alter the display of molecules in an HTML page:

Using either of these methods, you can create buttons that change display methods or display options, highlight specific groups of atoms, perform discrete rotations, etc. To learn more about RasMol scripting, download the RasMol manual and then check out our RasMol scripting tutorial for a general introduction. For more detail, please see Eric Martz's Chime pages. To investigate CSML scripting, look at the following CSML reference and then check out an interactive Chime paper by Peter Nixon, Christopher Leach and Henry Rzepa, which incorporates CSML buttons.

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Troubleshooting

Chime works fine for local files and files on other servers, but displays a "broken plug-in" when the files are on my server.

See How do I make my server understand the various chemical MIME types? under Installation and Configuration.

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On the Macintosh, sometimes I get a broken plug-in icon instead of a structure. Why?

Please use Netscape Navigator 3.04 or Netscape Communicator 4.04.

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Chime doesn't work with a network installation of Netscape Navigator

Chime needs to access the files it displays from the disk cache. Set "Options" "Network Preferences" "Disk Cache Directory" to a writable directory, either on your Network File Server or on a local hard drive. Make sure the cache size is > 0. A top-level directory may not work while a subdirectory is more likely to work.