Troubleshooting Broken PiPEs
- My command script doesn't give the expected molecular view.
Preferences to designate
yourself as an expert. After you run the offending script, use the
option (below the message box) Edit script to view the script
that is being executed. Simply examining the script closely may reveal
the problem. Of course, you can actually edit it and try the changes.
Desired changes would then have to be edited into the script in the
PiPE Block of the *_pipe.pdb file.
- When you click the link to start a PiPE chapter, a
new window opens for PE, two frames appear, the right frame turns
black with MDL in the lower right, and nothing else happens.
colon at the end) in the location slot at the top of the browser, and press Enter.
to clear all the messages in the js console, many of which may have accumulated
earlier and be irrelevant. Close the stalled PiPE window and
attempt to re-start it. Now examine the reports in the js console.
In Netscape 7 and Mozilla one harmless "unhandled exception" error occurs
normally during PE startup and can be ignored. (In Firefox, three occur.)
If another kind of js error is reported, hopefully it will help you
Example: If you fail to quote the title, a fatal js error occurs stalling
!js pipe_title = Structure of Collagen // fatal js error
!js pipe_title = "Structure of Collagen" // OK
I moved the folder containing my PiPEs. It worked fine
before I moved it but now it doesn't start.
In order for PiPEs to work, there must be a copy of Protein Explorer
on the same computer or server, and it must be "side by side"
with the directories
my_molecules/pipes/, which must begin with exactly the directory names
For example, these two must be side by side in the same directory:
Then, make sure that the file
is present and correctly defines the path from itself to PE in
the variable pe_path. In the example
above, the correct path would be "../../protein_explorer_2.73_alpha/".
You can have multiple versions of PE side by side; pe_path specifies
which version your PiPEs will employ.
Finally, make sure the paths to the files pe_path.js and pstart.js in
pipes/template are correctly specified in the index.htm file in
your PiPE. For example, if your PiPE is in
then index.htm must contain near the top
The number of steps back ("../") to template must be correct.
See also publishing your PiPEs on a server.
- When I save a PiPE PDB file from PE (Chime) onto a Macintosh,
the filename is truncated. When I load the saved file into PE,
it fails with an error message that the filename should end in "_pipe.pdb".
Netscape 4.8 (running in Classic) under Mac OSX cannot handle filenames
longer than 31 characters. Thus, a file named
"1ucy_consurf_1111617002_pipe.pdb" (32 characters long) will be saved
"1ucy_consurf_1111617002_pipe.pd" (31 characters long) with the final "b"
truncated. If you rename the file, adding the final "b", attempting to
load it into Empty PE with the Browse button will produce a strangely
corrupted filename. The solution is to use shorter filenames (less than
or equal to 31 characters).
- More troubleshooting hints may be added here in a future revision.
Send your suggestions to firstname.lastname@example.org.