[Proteopedia] Jmol version problems in Proteopedia

[Eric Martz]

Hello, Proteopedia users,

On Wednesday (3 days ago), an attempt was made to upgrade the Jmol 
applet in Proteopedia from 11.6.14 (which has been in use there since 
early 2009, to the current stable release, 11.8.7. Within 24 hours, a 
number of problems were discovered, and the Jmol in Proteopedia was 
rolled back to 11.6.14.

Two of us who use OS X found that after the rollback, the old Jmol 
did not reappear in our browsers despite clearing of the browser and 
java caches. (Jmol applet reports its version when you click on 
"Jmol" to the lower right of the molecule, then on "About Jmol".) 
Yesterday I discovered that the java cache was not being cleared by 
the "Jmol Preferences.app", and figured out how to clear it manually 
(using a couple of unix commands in Terminal). If any of you have 
this problem, let us know and I'll post instructions here.

Currently, when you "Export this page", the exported (downloaded) 
article is accompanied by Jmol 11.8.7. (This was done temporarily for 
debugging purposes). Sometimes, the initial scenes are incorrect with 
Jmol 11.8.7, and animations that should start automatically do not do 
so. If you need to export a page before we roll back the Jmol in the 
export mechanism, it is easy to substitute Jmol 11.6.14 for 11.8.7 -- 
ask here and I'll provide step by step instructions.

We sincerely apologize for these inconveniences!

Yours truly, - Eric

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Eric Martz, Professor Emeritus, Dept Microbiology
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