Important: Using Netscape 4.8 here will save you considerable editing in step #6 below. Both Gecko browsers and Microsoft Internet Explorer change links from relative (which work off-line) to absolute (on-line), requiring tedious repairs in step #6 below.

Unfortunately, during saving to disk, some browsers convert the relative links to these files to absolute links back to the ConSurf server on-line. You could use an HTML editor to change these links to the local files.

1. Copy or move your job output pdb file into the job folder. (This is the file with a name in the format 1xxx_consurf0000000000_pipe.pdb.)

2. Use a text editor to modify the file output.html as follows.

3. Paste the following two lines just above the line "</head>". Note that the relative filepaths in the following examples assume that you saved your files in the path indicated in step #1 above.

   <script src="../template/pe_path.js"></script>
   <script src="../template/pstart.js"></script>

4. Change the "href" for the link to Protein Explorer to this:

   <A HREF="javascript: start_pe('1xxx_consurf0000000000_pipe.pdb');">

   where the filename matches the actual PDB filename.

Organizing your saved ConSurf results with a page of links.

For PDB files only:

1. These instructions assume you have collected the ConSurf PDB files in the folder my_molecules/pipes/my_consurfs.
2. Copy the file my_molecules/pipes/consurf/index.htm into my_consurfs.
3. If you have not already done so, create the file mypipes.htm in the folder my_molecules/pipes. Here are instructions.
4. Use an HTML editor program or a plain text editor program, as you prefer, to add a link to my_consurfs/index.htm in the file my_molecules/pipes/mypipes.htm.
5. Use your editor to change the links in my_consurfs/index.htm to go to your downloaded ConSurf PDB files. Delete what isn't applicable, add notes about your ConSurf results, etc. as you wish.
6. Now you can access your downloaded ConSurf PDB files from the PE FrontDoor by clicking on Presentations in PE, then Examples, then My PiPEs, then the link you made there.

For all job results:

1. These instructions assume you followed the above instructions and put your job results files into a folder with a name of the format 1xxx_a_consurf, inside the folder my_molecules/pipes. Substitute the real name(s) of your folder(s) below.
2. If you have not already done so, create the file mypipes.htm in the folder my_molecules/pipes. Here are instructions.
3. You could put the links to your saved jobs in mypipes.htm. Alternatively, especially if you plan to save lots of ConSurf jobs, or create PiPEs that are not simply ConSurf results, you can create a separate HTML file just for ConSurf jobs.
   If you prefer the latter, copy the file mypipes.htm to myconsurfs.htm. Then, using an HTML editor program, make a link in mypipes.htm to myconsurfs.htm.
4. Using an HTML editor program, make link(s) in mypipes.htm (or myconsurfs.htm) to the index.htm file(s) in your 1xxx_a_consurf folder(s).
5. Optionally you can annotate your consurf results in mypipes.htm (or myconsurfs.htm).
6. To access your saved ConSurf results, at PE's FrontDoor, click on Presentations in PE (right hand gray box), then Examples, then My PiPEs (and if you made a separate file myconsurfs.htm, on the link you made to that file).

Changing the conservation color scheme.

!color color_grade0 A1004A insufficient data 
!color color_grade1 FFC600 variable
!color color_grade2 D7A800
!color color_grade3 977200
!color color_grade4 5B6800
!color color_grade5 5B6800
!color color_grade6 5B6800
!color color_grade7 5E8A00
!color color_grade8 43BF00
!color color_grade9 00FF00 conserved

Standard color key (protexpl/consurf/colorkey.gif, isd.gif)

Alternate color key (protexl/consurf/altkey.gif, altisd.gif)

If you create a customized color key, you tell PE to use it by adding these two lines in the PiPE block of the PDB file header. Add the lines below just after the line
!! Specify the custom consurf control panel:

! consurf_color_key = "altkey.gif";
! consurf_isd_color_key = "altisd.gif";

Customizing the ConSurf control panel.

! pipe_cp1 = "consurf/consurf.htm";