[Molvis-list] Bug fixed in PE 2.721

Eric Martz emartz at microbio.umass.edu
Mon Feb 21 14:40:04 EST 2005

Protein Explorer (PE) 2.72, released 16 hours ago, had this bug: If you 
started Empty Explorer, then loaded an ordinary PDB file (not a PiPE) by 
any of the four mechanisms at the "Load Molecule" control panel, the 
FirstView rendering failed to display. Thanks to Gabriel Pons for reporting 
this so quickly! This bug has been fixed in PE 2.721, just released and 

When you download this (or a future) new version of PE and install it, it 
will create a new folder, in this case "Protein Explorer 2.721 Alpha", 
leaving your previous version intact (which you may delete later). It will 
also overwrite all of the downloaded files in the folder "my_molecules" and 
its subfolders. Provided you have followed the instructions in PE 2.72 for 
setting up your own PiPEs, they will not be affected, but will be 
redirected to work with the new version of PE.

Technical info about the way this works: PiPEs you create are put in new 
folders, e.g. my_pipe1, which do not exist in the download, so are not 
overwritten. However, all PiPEs use the file 
my_molecules/pipes/template/pe_path.js in order to locate PE. This file is 
updated with each download of a new version. Thus, existing PiPEs you 
created will use the new version of PE automatically.

Similarly, links to PiPEs you create are not affected: The downloaded 
document my_molecules/pipes/example.htm contains a link to "My PiPEs" which 
goes to a non-existent document my_molecules/pipes/mypipes.htm. When you 
create PiPEs, the links to them are created in mypipes.htm, which you first 
create by copying the downloaded file my_molecules/pipes/blank.htm. Again, 
since mypipes.htm is not included in the downloaded, your links to your 
PiPEs are not affected.

You can always get to your PiPEs from the FrontDoor of your downloaded PE 
by clicking "Presentations in PE", then "Example PiPEs", then "My PiPEs".


Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US

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