Proteopedia:Problems: Difference between revisions
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== Problems, less urgent== | == 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 http://proteopedia.org/wiki/index.php/4cpa] vs. [http://proteopedia.org/wiki/index.php/4CPA http://proteopedia.org/wiki/index.php/4CPA]. [[User:Eric Martz|Eric Martz]] 03:39, 2 January 2010 (IST) | <span style="background-color:yellow;color:green">'''SOLVED'''</span> '''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 http://proteopedia.org/wiki/index.php/4cpa] vs. [http://proteopedia.org/wiki/index.php/4CPA http://proteopedia.org/wiki/index.php/4CPA]. [[User:Eric Martz|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. [[User:Emartz|Emartz]] 19:32, 28 February 2008 (IST) | <span style="background-color:yellow;color:green">'''SOLVED'''</span> '''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. [[User:Emartz|Emartz]] 19:32, 28 February 2008 (IST) -- On seeded pages using now only singular of a word [[User:Jaime Prilusky|Jaime Prilusky]] 21:26, 24 January 2018 (UTC) | ||
: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. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (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. --[[User:Ralf Stephan|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]]). [[User:Eric Martz|Eric Martz]] 23:48, 4 January 2011 (IST) | <span style="background-color:yellow;color:green">'''SOLVED'''</span> '''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]]). [[User:Eric Martz|Eric Martz]] 23:48, 4 January 2011 (IST) | ||
'''<font color='red'>Error: 0 ()</font>''' appears just below the ''search'' slot at left when you enter text, then press the Enter key. It would be nice to eliminate this. [[User:Eric Martz|Eric Martz]] 00:15, 3 January 2010 (IST). Please confirm: Always occurs on Safari (Mac), never on Firefox (Mac) or Explorer (Windows XP) [[User:Jaime Prilusky|Jaime Prilusky]] 07:43, 10 January 2010 (IST) Yes, I agree. [[User:Eric Martz]]. | '''<font color='red'>Error: 0 ()</font>''' appears just below the ''search'' slot at left when you enter text, then press the Enter key. It would be nice to eliminate this. [[User:Eric Martz|Eric Martz]] 00:15, 3 January 2010 (IST). Please confirm: Always occurs on Safari (Mac), never on Firefox (Mac) or Explorer (Windows XP) [[User:Jaime Prilusky|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? [[User:Emartz|Emartz]] 17:36, 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? [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST) | ||
'''Search interface improvement:''' Improve the ‘Search’ option that is above the Google one on side of every page? If someone searches 'ribosome', and presses `Search` instead of pressing 'Go' in the top search bar on Proteopedia, they don't get the Ribosome page at the top, [[http://proteopedia.org/wiki/index.php/Special:Search?search=ribosome&fulltext=Search result of searching ribosome]]. [[User:Wayne Decatur|Wayne Decatur]] 16:46, 23 January 2018 (UTC) | |||
<span style="background-color:yellow;color:green">'''SOLVED'''</span> '''Category page issue:''' On the [[:Category:Ribosome|ribosome category page]] that is the top search result, the [[Ribosome|Ribosome topic page]] isn't even listed there. A more general problem than just the Ribosome page?[[User:Wayne Decatur|Wayne Decatur]] 16:46, 23 January 2018 (UTC) -- Was missing <nowiki>[[Category:Ribosome]]</nowiki> on the page [[User:Jaime Prilusky|Jaime Prilusky]] 21:26, 24 January 2018 (UTC) | |||
'''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. [[User:Emartz|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. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST) :Partial solution available at [[http://proteopedia.org/wiki/index.php/Special:CategoryTree Special:CategoryTree]] [[User:Jaime Prilusky|Jaime Prilusky]] 08:00, 3 January 2010 (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. [[User:Emartz|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. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST) :Partial solution available at [[http://proteopedia.org/wiki/index.php/Special:CategoryTree Special:CategoryTree]] [[User:Jaime Prilusky|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 --[[User:Eran Hodis|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. --[[User:Wayne Decatur|Wayne Decatur]] 4:27, 28 September 2009 (EST) ) | '''Structure sections seems to interfere with browsing back:''' Possible to make it so the structure section goes back to where user was in article and not to the top of the structure section when using browser ‘Back’ button? Example page, the [[Ribosome|Ribosome page]], if you click link to scene about structural detail of active site and then try to go back. Or would [[Ribosome|Ribosome page]] page maybe be good test of better design. It seems someone put everything after start in a structure section?[[User:Wayne Decatur|Wayne Decatur]] 16:46, 23 January 2018 (UTC) | ||
<span style="background-color:yellow;color:green">'''SOLVED'''</span> '''Scene links that have green displayed text that includes non-alphabetical characters like ampersands and greek letters''' do not display properly --[[User:Eran Hodis|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. --[[User:Wayne Decatur|Wayne Decatur]] 4:27, 28 September 2009 (EST) ) Accented characters are Ok. Use HTML entities for ampersand, greek and other special characters [[https://www.w3schools.com/charsets/ref_utf_greek.asp]] like &beta; for β. [[User:Jaime Prilusky|Jaime Prilusky]] 13:06, 17 October 2018 (UTC) | |||
'''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 [http://bioportal.weizmann.ac.il/oca-docs/fgij/bigpdb.htm tests with big PDB files] and a [http://bip.weizmann.ac.il/oca-docs/PDBRecNamStats/PDBSizeDistribution.html list of the largest files in the PDB]. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 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 [http://bioportal.weizmann.ac.il/oca-docs/fgij/bigpdb.htm tests with big PDB files] and a [http://bip.weizmann.ac.il/oca-docs/PDBRecNamStats/PDBSizeDistribution.html list of the largest files in the PDB]. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 2008 (IDT) | ||
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<u><i>Workaround</i></u>: Add an all-encompassing range (it can be outrageously large, such as '1-8000:a') in front of the colon and chain designation. [[User:Wayne Decatur|Wayne Decatur]] 08:24, 11 October 2009 (IST) | <u><i>Workaround</i></u>: Add an all-encompassing range (it can be outrageously large, such as '1-8000:a') in front of the colon and chain designation. [[User:Wayne Decatur|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 --[[User:Eran Hodis|Eran Hodis]] 16:20, 17 June 2008 (IDT) | <span style="background-color:yellow;color:green">'''DISREGARDED:'''</span> '''Green (initial scene) link in structure box''' should recall the user specified initial scene rather than the default Proteopedia initial scene --[[User:Eran Hodis|Eran Hodis]] 16:20, 17 June 2008 (IDT) The structure box is not longer in use [[User:Jaime Prilusky|Jaime Prilusky]] 13:09, 17 October 2018 (UTC) | ||
'''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. [[User:Eric Martz|Eric Martz]] 00:44, 2 May 2012 (IDT) | |||
<span style="background-color:yellow;color:green">'''DISREGARDED:'''</span> '''Jmol animations sometimes fail to start:''' Example: green links in the section "Opening and Closing" at [[Mechanosensitive channels: opening and closing]]. [[User:Eric Martz|Eric Martz]] 00:48, 2 May 2012 (IDT). Not longer happens with Proteopedia at AWS and the current JSmol version. [[User:Jaime Prilusky|Jaime Prilusky]] 13:11, 17 October 2018 (UTC) | |||
<span style="background-color:yellow;color:green">'''SOLVED'''</span> '''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. --[[User:Ralf Stephan|Ralf Stephan]] 11:38, 17 February 2009 (IST) | <span style="background-color:yellow;color:green">'''SOLVED'''</span> '''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. --[[User:Ralf Stephan|Ralf Stephan]] 11:38, 17 February 2009 (IST) | ||
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'''<nowiki><references /></nowiki> disappear''' when placed ''after'' a <nowiki><div></nowiki> tag, see a minimal test case at [[User:Wayne Decatur/Sandbox RefErrorReDo]] [[User:Wayne Decatur|Wayne Decatur]] 17:08, 24 November 2010 (IST) | '''<nowiki><references /></nowiki> disappear''' when placed ''after'' a <nowiki><div></nowiki> tag, see a minimal test case at [[User:Wayne Decatur/Sandbox RefErrorReDo]] [[User:Wayne Decatur|Wayne Decatur]] 17:08, 24 November 2010 (IST) | ||
<span style="background-color:yellow;color:green">'''SOLVED'''</span> '''problems with scenes changing unexpectedly''' appear in the first applet on the [http://proteopedia.org/wiki/index.php?title=Aconitase&oldid=930869 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. --[[User:Ralf Stephan|Ralf Stephan]] 18:37, 21 February 2009 (IST) | <span style="background-color:yellow;color:green">'''SOLVED'''</span> '''problems with scenes changing unexpectedly''' appear in the first applet on the [http://proteopedia.org/wiki/index.php?title=Aconitase&oldid=930869 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. --[[User:Ralf Stephan|Ralf Stephan]] 18:37, 21 February 2009 (IST) | ||