Proteopedia:Problems
This page is for listing problems in existing features. Please list desired new features on the page Proteopedia:Wishlist
When a problem below has been fixed, please prefix it with "Fixed (date):", rather than deleting it from this page. In this way everyone knows what problems have been fixed and when.
Problems that need fixing before widespread announcementProblems that need fixing before widespread announcement
SOLVED Green links need to work in Firefox version 2, with Java version 1.60_03 and higher! --working on it --Eran Hodis 20:13, 12 April 2008 (IDT)
Help: Searching needs to be revised to agree with the actual search behavior (which needs careful testing) and to explain the limitations and advantages (with examples) of the WikiMedia Search (as modified) vs. the Google search. Eric Martz 19:20, 13 April 2008 (IDT)
SOLVED (Pages in the User namespace can now have Jmol Scenes) Document that pages in the User: namespace cannot have Jmol scenes, or else enable that. It seems natural for users to put scenes on their personal pages. If it is to remain disabled, then the SAT should not be openable, and instead a message of explanation should appear where the SAT +/- normally is. Emartz 20:50, 26 March 2008 (IST)
SOLVED Searching for "Sandbox" fails to find either the page titled "Sandbox" or the page titled "Sandbox 2". And searching for "sandbox" also fails, despite that word occuring in the text of each page! Emartz 03:25, 26 March 2008 (IST) Solved by Anat Kats and J Prilusky 26 March 2008
SOLVED The format of Jmol's hover report needs to be correct on all pages. Currently it is incorrect on the main page. Emartz 02:38, 16 March 2008 (IST) Solved by Eran 25 March 2008 -- let me know if problems with hover surface again
SOLVED Search result ordering: list pages that don't begin with a numeral before pages that do. Example: Search for "mhc". The page "Major histocompatibility complex class I" appears almost at the end of the 400-some length list, curiously before 3c9n. Emartz 17:36, 28 February 2008 (IST). Solved by Anat Kats and J Prilusky 25 March 2008
SOLVED Singular vs. plural in searches: Searching for "antigens" fails to find "Category:Histocompatibility_antigen", but searching for "antigen" finds it. Ideally, relevant pages should be found regardless of whether the query term is singular or plural. Emartz 02:44, 16 March 2008 (IST). Solved by J Prilusky 25 March 2008
Jmol Extensions need to work. Example of non-working checkboxes: Nucleosomes#Scenes_for_Projection_in_Biochemistry_Classes. The checkboxes appear but checking them does not send the script to Jmol. I note this item concerning the installation of Jmol extensions:
- Add the following line to the end of LocalSettings.php:
- require_once('extensions/Jmol/Jmol.php');
This is here under Installation: wiki.jmol.org/index.php/MediaWiki Emartz 22:06, 28 February 2008 (IST)
Namespace lists: PARTIALLY SOLVED, see Proteopedia:Namespaces but the links don't work. Need a way to list namespaces, and pages within each namespace. For example, see Wikipedia: Namespace. Perhaps this should be an item on the the left, similar to "Special Pages". I see no way to list the pages within a namespace (to find out what they are). The "Special pages" do not seem to include such lists. If I use the checkboxes on the search results page to limit a search to the Proteopedia namespace, and search for "proteopedia", I get 4 hits (Troubleshooting, Policy, Wishlist, Problems). But there may be other pages in this namespace that don't explicitly mention the query term, which therefore will not appear on the search results list. Namespaces are rather important for authors to know about. That is why I think a way to list these pages is a high priority. Emartz 17:36, 28 February 2008 (IST)
Problems that can be fixed after widespread use beginsProblems that can be fixed after widespread use begins
Category: singular vs. plural: Category:Nucleosome and Category:Nucleosomes are two separate pages with nonoverlapping contents. It would be great if all pairs of the same term +/- a terminal "s" can be merged into a single page per such pair. Emartz 19:32, 28 February 2008 (IST)
Search result ordering: Perhaps PDB code-titled pages should be ordered to show those with the most hits of the search term above those with fewer hits? Emartz 17:36, 28 February 2008 (IST)
Special pages > Categories: This very long list needs a mechanism to jump to a letter of the alphabet. Otherwise, it is unusable because it has tens of thousands of items. Emartz 17:36, 28 February 2008 (IST)
Scene tags placed in a bulleted list don't display as green links. Emartz 17:36, 28 February 2008 (IST) Workaround: Use standard bullet list HTML notation instead of wikitext markup J Prilusky 9:11 3 March 2008
Scenes that have green displayed text that includes non-alphabetical characters like ampersands and greek letters do not display properly --Eran Hodis 17:24, 12 June 2008 (IDT)
Models with >100,000 atoms fail to display due to java memory limitations. These are <0.1% of the PDB. I suggest that a box be inserted automatically (from a template) on such pages that explains why Jmol remains blank. We should test whether increasing the memory allocated to java reduces this problem, and if so, provide an explanation of how to increase java memory in Win and OS X. See also tests with big PDB files and a list of the largest files in the PDB. Eric Martz 19:20, 13 April 2008 (IDT)