Protein Explorer Advisories
Updated July 7, 2009

Issues have arisen beginning in 2007, and more recently, that create problems for Protein Explorer. Because tools that work better are now available, I am no longer maintaining Protein Explorer. (Eventually I hope that a Protein Explorer in Jmol will become available, but I am not developing one. Volunteers should contact hansonr at stolaf dot edu.) Until further notice, this Advisories page is the only place where the recent problems are explained, and solutions are provided (where available). Note that these problems and solutions are not documented within Protein Explorer.

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In Protein Explorer:
  1. For downloaded PE (but not for online PE), some recent versions of Firefox don't work because they don't allow you to turn off the popup blocker for local files. Specifically, 3.0.11 (and perhaps some earlier versions) has this problem, while 3.0.7 (and perhaps some later versions) does not.
    • Solution 1: disable the popup blocker completely (Tools, Options, Content, uncheck Block pop-up windows.)
    • Solution 2: Download and install an older version of Firefox. If, during installation, you specify a different directory, e.g. "Firefox 3.0.7", then you can have both the older version and the current version installed and available.
    (Thanks to Colleen Carpenter for calling this to my attention in early July, 2009, and for the link to older versions of Firefox.)

  2. Saving MolSlides is broken. This came to my attention in October, 2008. (PE saves a zero length .htm file.) Unless I hear from a number of users, I do not plan to fix this. Instead, I strongly recommend that you use Proteopedia.Org. There you can make great presentations much more easily than MolSlides, and they are online and available to anyone instantly. You can protect pages that you create so only you can edit them, if you wish.

  3. Internet Explorer Seven (7) (Windows) does not work with Protein Explorer. Although Chime 2.6 SP7 was released in August, 2007, to support Internet Explorer 7, Protein Explorer has not been upgraded to use this version of Chime. Firefox is free and is recommended for Protein Explorer. If you are unable to use Firefox or Internet Explorer 6 on your Windows computer, we regret being unable to provide a Protein Explorer that you can use.

  4. Chime 2.6 SP6 must be used with Internet Explorer Six (6) and Firefox (Windows). Note that SP6 is NOT the latest version of Chime available for download, but it IS available at MDL's Chime download site. If you installed Chime recently, but Protein Explorer says
      Sorry, but either the Chime plugin is not installed in your browser, or it is not sufficiently recent to work with Protein Explorer.
    then most likely you installed SP7 or later. To check the version of Chime installed in your browser:
    • Go to our Chime Test Site.
    • If you don't see the pink ball, you don't have Chime installed in this browser.
    • If you see the pink ball, right-click on it, and then, on the menu that appears, click on About..., and Chime's version is displayed.

  5. If you are using Mac Classic (OS9) with Netscape Communicator 4.8, please continue to use Chime 2.6 SP4, which is the most recent release for Macs.

  6. DNA is not correctly displayed by Protein Explorer in PDB files remediated by the Protein Data Bank. All files obtained from the World Wide Protein Data Bank since August 1, 2007, are remediated. When you type a PDB identification code into the FrontDoor of Protein Explorer, you now get the remediated PDB file. This problem is within MDL Chime, and is not under our control. If you need to explore a molecule containing DNA, here are two solutions:

    • Use FirstGlance in Jmol instead of Protein Explorer. It works much better with the DNA in remediated files. It does noncovalent bonding "contacts" analyses similar to those of Protein Explorer. Although it does not let you make customized molecular views, those can be made easily at Proteopedia.Org, and at publication quality with Polyview-3D.

    • If your DNA-containing PDB file was published before August 1, 2007, use the unremediated PDB file.

Proceed to the Protein Explorer FrontDoor