Proteopedia:Problems

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This page is for listing problems or bugs in existing features of Proteopedia. Please list desired new features on the page Proteopedia:Wishlist

When a problem below has been fixed, please prefix it with "Solved", rather than deleting it from this page. In this way everyone knows what problems have been fixed and when. Also please add a note giving the date when it was fixed/solved.

Problems, more urgent

SOLVED Non-standard residues should be limited to residues that are also protein or nucleic. For example in 1au1, BGC and G6D are carbohydrate and hence should be listed under Ligands instead of Non-Standard Residues. (See Non-Standard Residues and Ligands for more examples.) Eric Martz 21:24, 21 March 2010 (IST). Solved by Jaime Prilusky 14:40, 22 March 2010 (IST) Page for 1au1 was reseeded. The correction will gradually propagate to other pages.

SOLVED Wrong chains: When you show Evolutionary Conservation for 4cpa, the chain toggle buttons are listed A, C, B, D. However, the actual chains in this PDB file are A, B, I, J. Similarly, the buttons are A, B for 1apm where the actual chains are E and I. Also 1acb where the chains are E and I (not A and B). Eric Martz 03:18, 2 January 2010 (IST) Solved by Jaime Prilusky 08:27, 3 January 2010 (IST) This is a related problem to the latest PDB file remediation. Solved for these structures but there might be others

SOLVED 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) This page appears to be in decent shape now. Eric Martz 23:39, 4 January 2011 (IST)

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)

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

SOLVED 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) Solved by Angel Herraez, 14-May-2009

SOLVED Namespace lists: 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) This appears to be solved: see Proteopedia:Namespaces. See also the use of Special:PrefixIndex at Proteopedia:Subdirectories. Eric Martz 23:37, 4 January 2011 (IST)

SOLVED On page 1c96, the ligand FLC (fluorocitrate?) is shown while, if you click on its green link, it's really a citrate. I don't know of other instances but I'll now look for them. --Ralf Stephan 19:22, 15 February 2009 (IST) ♣ Ligand green links are generated from the PDB file. I checked the PDB file, and what is being displayed matches the PDB file. If this is really an error then please notify the PDB. They can fix the file, and we will update the page accordingly. --Eran Hodis 20:40, 15 February 2009 (IST) ♣ This is not really a problem. PDB (RCSB) is not required to name ligands and short molecules following any known nomenclature. In the structure file for 1c96 you may find this line: HETNAM FLC CITRATE ANION from where OCA gets the name for Proteopedia. Other interesting example can be found in structure 1yuh, featuring Np, the official symbol for Neptunium to indicate 3-nitropropanoic acid. Jaime Prilusky Sun Feb 15 22:01:33 IST 2009

Problems, less urgent

PDB code case: Lower case PDB codes work in internal links, e.g. 4cpa, but upper case codes don't, e.g. 4CPA. Similarly, links to Proteopedia from outside have the same problem, e.g.http://proteopedia.org/wiki/index.php/4cpa vs. http://proteopedia.org/wiki/index.php/4CPA. Eric Martz 03:39, 2 January 2010 (IST)

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)

As this is a pressing problem that only can be gotten right with human intervention, I'd suggest at least a user-editable synonyms list that contains such many-to-one relationships---a sort of dictionary, if you will, that is used before finally applying a category to a PDB. --Ralf Stephan 19:00, 18 February 2009 (IST)

Problem with lower case chain IDs: PDB files can have up to 62 chains, each with an alphanumeric ID (Jmol/Visualizing large molecules). Typically, the first 26 are given ID's A-Z, and the next 10, ID's 0-9. Above 36 chains, lower case letters a-z must be used, and sometimes they are used without numerals, and/or without using all 26 upper case letters (1tzn). Proteopedia displays one toggle button per chain in its Evolutionary Conservation display. Currently, the Jmol mode set chainCaseSensitive is not in use. Therefore, when the same letter identifies two different chains (distinguished by case), the toggle buttons fail. An example is 2zkr, the only PDB entry with 62 chains (in January 2011). Also in some cases, the toggle buttons have the wrong letter or wrong case (1tzn). Eric Martz 23:48, 4 January 2011 (IST)

Error: 0 () appears just below the search slot at left when you enter text, then press the Enter key. It would be nice to eliminate this. Eric Martz 00:15, 3 January 2010 (IST). Please confirm: Always occurs on Safari (Mac), never on Firefox (Mac) or Explorer (Windows XP) Jaime Prilusky 07:43, 10 January 2010 (IST) Yes, I agree. User:Eric Martz.

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) :Until we have the alphabet, there is a workaround, see my user page, where I have three such searches edited to my liking. You can do that too, just by editing such a link in your browser URL line. --Ralf Stephan 19:00, 18 February 2009 (IST) :Partial solution available at [Special:CategoryTree] Jaime Prilusky 08:00, 3 January 2010 (IST)

Scene links 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) (So if you try to add angstrom sign by code Å sometimes it will cause that green link not to show up and sometimes even throws an XML error when you try to save the page. --Wayne Decatur 4:27, 28 September 2009 (EST) )

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)

Toggles made with Templates fail if they include a selection of a chain with no range in front of the colon, for example 'select :1' or 'select :a'. Wayne Decatur 08:24, 11 October 2009 (IST) Workaround: Add an all-encompassing range (it can be outrageously large, such as '1-8000:a') in front of the colon and chain designation. Wayne Decatur 08:24, 11 October 2009 (IST)

Green (initial scene) link in structure box should recall the user specified initial scene rather than the default Proteopedia initial scene --Eran Hodis 16:20, 17 June 2008 (IDT)

Double-zoom transition: Certain scene-transitions zoom out twice -- once is what is desired. Examples: Nitrotyrosine green link "pushes". Lac repressor section DNA Kinks, green link "2 leucines". The induced fit morph at Avian Influenza Neuraminidase, Tamiflu and Relenza. We should wait until the new scene-storing mechanism using .jmol files is in place -- then address this if necessary. Eric Martz 00:44, 2 May 2012 (IDT)

Jmol animations sometimes fail to start: Example: green links in the section "Opening and Closing" at Mechanosensitive channels: opening and closing. Eric Martz 00:48, 2 May 2012 (IDT)

SOLVED Gzipped PDBs should be accepted since Jmol accepts them as they are. I have here a 11,5 MB morph that when gzipped is only 2,8 MB. I don't want to upload nor download four times the amount for no reason. --Ralf Stephan 11:38, 17 February 2009 (IST)

You should now be able to upload gzipped PDBs. --Eran Hodis 19:07, 17 February 2009 (IST)

SOLVED Internal [[links]] don't work when in an applet text string. --Ralf Stephan 19:00, 18 February 2009 (IST) -- Thanks for finding this bug Ralf. Actually internal links were working in applet captions, but not in applet captions that specified an initial scene rather than the default view. Now fixed. --Eran Hodis 19:18, 18 February 2009 (IST)

SOLVED <references /> disappear when placed after a second <applet>, see a minimal test case at User:Ralf_Stephan/Sandbox_2. --Ralf Stephan 10:32, 21 February 2009 (IST)

Thanks, fixed. --Eran Hodis 18:01, 7 March 2009 (IST)

<references /> disappear when placed after a <div> tag, see a minimal test case at User:Wayne Decatur/Sandbox RefErrorReDo Wayne Decatur 17:08, 24 November 2010 (IST)

SOLVED problems with scenes changing unexpectedly appear in the first applet on the aconitase (older version) page. There are 3 green links, and if you click 1,2,1,2,1... the two scenes will stay as they show the first time clicked, but as soon as you click 3, 2 will appear different (the three yellow amino side chains around the cluster lack several atoms/bonds then). I have a problem with 3, too, as it doesn't show as it was saved, but this is more elusive at the moment. --Ralf Stephan 18:37, 21 February 2009 (IST)

I'm pretty sure that this has been solved. If not, please edit this post --Eran Hodis 14:58, 11 January 2010 (IST)

SOLVED 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. Solved by Jaime Prilusky 21:30, 13 December 2009 (IST)

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Jaime Prilusky, Eran Hodis, Ralf Stephan, Wayne Decatur, Angel Herraez

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