A hyperlink to Protein Explorer (PE) which prespecifies a molecule (PDB file) actually contains two URL's

1. URL to PE, or PE-URL
2. URL to PDB file, or PDB-URL

Never* use a target in the anchor! Use of a target defeats the ability to have multiple PE windows running concurrently.
    <a href="...">correct anchor format</a>
    <a href="..." target="window_name">INCORRECT anchor format</a>

*There is one exception: When making a hyperlink to PE version 1.0 on an RCSB (or RCSB mirror) server, you should use a target.

The original folder/directory containing PE at UMass was named explorer and that name has been kept to avoid breaking hyperlinks and bookmarks. It is now recommended that all new installations of PE be put in a folder named protexpl to avoid confusion with the Microsoft Windows desktop operating system, which is named explorer. The downloadable package for PE was named explorer.exe but a file of this name inadvertantly placed in C:\ prevents Windows from booting! Therefore the downloadable PE package is now named protexpl.exe; the folder into which it is unpacked should be named protexpl to minimize confusion.

The following numbered list summarizes the general formatting rules. More details are given below for some cases.

1. When the source of the PDB file(s) is the Protein Data Bank, the PDB-URL should give only the four-character PDB ID ("pid") code(s). For example, the URL will end in /protexpl/pe.htm?id=pid1& for the Explorer, and in /protexpl/pe.htm?id=pid1&id2=pid2& for the Comparator. If the PE-URL specifies one of the Protein Data Bank servers or mirrors, the PDB files will automatically be fetched from the same location. When the PE-URL specifies a local installation, or a non-PDB server, this type of 4-character specification allows each client to set, as a PE preference, their preferred PDB mirror site from which the PDB files will be fetched via Internet.

2. When the source of the PDB file(s) is not the Protein Data Bank, the URL must be given for each PDB. Thus, the hyperlink will be of the form /protexpl/pe.htm?id=url1& for the Explorer, and /protexpl/pe.htm?id=url1&id2=url2& for the Comparator.

3. When the PDB-URL begins with http:// (or ftp://) the colon must be escaped to %3A and if the PDB URL contains a query parameter, the question mark must be escaped to %3F. Do not escape slashes or the equals sign. Moreover, when there are several query parameters, the PDB filename must be the last item at the end of the PDB URL. For example if the PDB-URL is
   http://pqs.ebi.ac.uk/pqs-bin/macmol-chime.pl?filename=1hho.mmol
   then a hyperlink would have this form
   http://www.umass.edu/microbio/chime/protexpl/pe.htm?id=http%3A//pqs.ebi.ac.uk/pqs-bin/macmol-chime.pl%3Ffilename=1hho.mmol&

4. Relative PE-URL's may begin with two dots, such as "../shared/1d66.pdb". These are taken to be relative to the source of PE itself; namely, the protexpl folder/directory. If PE is coming from a server, relative URL's designate files on the server. If PE is coming from an installation on the local hard disk, relative URL's designate files on the local hard disk. Example: /protexpl/pe.htm?id=../shared/1d66.pdb&

5. Windows only: in PDB-URL's designating files on the local hard disk, colons following the disk drive letters should be changed to vertical bars (change C: to C|). This is not always necessary but the colon doesn't always work in earlier versions of Netscape. (The colons in http:// and file:/// should remain as colons.) Example: http://www.umass.edu/microbio/chime/explorer/pe.htm?id=c|/pdb_files/1b07.pdb&

6. Windows only: in references to PDB files on the local hard disk, backslashes delimiting folder names should be changed to foreslashes, e.g. c:\chime\protexpl should be given as c|/chime/protexpl. See complete example under previous paragraph.

7. Macintosh only: colons which delimit folder names should be changed to slashes. For example, "Macintosh HD:Chime:protexpl" should be given as "Macintosh HD/Chime/protexpl".

8. Filenames ending in .pdb: URL's ending in .pdb confuse Windows Netscape when the URL references a local file; therefore you should add an amperesand (&) to the end of any such URL. Thus a url ending in .pdb will not work in all cases while one ending .pdb& does.

PDB ID codes are 4-character codes which uniquely identify all structures available from the Protein Data Bank. 4-character molecule identifiers are taken by the Protein Explorer/Comparator (PE) to be PDB ID codes; PE offers to fetch the PDB files via Internet from the Protein Data Bank. The files are actually fetched from whichever PDB mirror site has been set in your PE preferences in a previous PE session.

Server URL. Thus, to pre-specify molecule 1d66 and invoke the Explorer, the URL is the path to the folder where PE is installed, plus pe.htm?id=1d66. So for example if you wish to use the PE from the UMass server, the URL is

www.umass.edu/microbio/chime/protexpl/pe.htm?id=1d66     Absolute URL

pe.htm?id=1d66     Relative URL

Local Filepath, Absolute. If you have installed PE locally in C:\Chime\protexpl or Macintosh HD:Chime:protexpl, the URL's would be

file:///C|/Chime/protexpl/pe.htm?id=1d66
file:///Macintosh HD/Chime/protexpl/pe.htm?id=1d66

Local Filepath, Relative. The above links are absolute, but links can also be relative (which enhances portability to another file tree). Suppose you have set up three folders as follows

../protexpl/pe.htm?id=1d66

Invoking Protein Comparator. Invoking the Comparator simply requires that two PDB ID codes be specified, which for the server URL above would be for example:

../protexpl/pe.htm?id=1lck&id2=1b07
www.umass.edu/microbio/chime/protexpl/pe.htm?id=1lck&id2=1b07

If you have saved PDB files to a local disk, you can use URL's to pre-specify particular files when invoking Explorer or Comparator. Below, we'll give only the Relative style of URL in the examples, but Local Filepath, Absolute or Server URL, Absolute styles can also be used.

For purposes of example, let's suppose you have created a folder under your "Chime" folder named "PDB Files", and into it downloaded two PDB files as follows:

Absolute PDB Filepaths. Absolute PDB filepaths can be used to invoke Explorer or Comparator respectively as follows. If you actually do create a "PDB Files" folder (see "Folder Tree Part II" above) and download 1lck and 1b07 into it from the PDB, the links below will work either from your local installation of PE, or when PE is being served from any server (provided it is in a folder named protexpl).

../protexpl/pe.htm?id=c|/Chime/PDB Files/1lck.pdb&
../protexpl/pe.htm?id=c|/Chime/PDB Files/1lck.pdb&id2=c|/Chime/PDB Files/1b07.pdb&
../protexpl/pe.htm?id=Macintosh HD/Chime/PDB Files/1lck.pdb&
../protexpl/pe.htm?id=Macintosh HD/Chime/PDB Files/1lck.pdb&id=Macintosh HD/Chime/PDB Files/1b07.pdb&

Relative PDB Filepaths. Using the folder tree specified in the above examples, relative PDB filepaths could be used in your /Chime/PDBLinks/PDBLinks.htm file as follows. Or, for test purposes, if you copied the present file (query_pe.htm) into such a Chime/PDBLinks folder and opened it in Netscape, and if the PDB files are present in the parallel Chime/PDB Files folder, and you have installed a local copy of the explorer in Chime/protexpl and Chime/shared, the links below should work. (In other words, they'll work if you have created the complete folder tree, Parts I plus II above, and appropriately filled each branch folder.)

../protexpl/pe.htm?id=../PDB Files/1lck.pdb&
../protexpl/pe.htm?id=../PDB Files/1lck.pdb&id2=../PDB Files/1b07.pdb&

pe.htm/?id=.../pdb_files/1cmk1atp.pdb