Proteopedia:Problems: Difference between revisions

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: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]].

Proteopedia:Problems: Difference between revisions

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 :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]].