How to see conserved regions: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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 ==My Molecule Has No ''Evolutionary Conservation'' Section in Proteopedia==
-If, in Proteopedia, the molecule of interest has no ''Evolutionary Conservation'' Section, calculate the conservation pattern yourself at the ConSurf Server. [[Quick ConSurf Analysis Procedure|Here are instructions.]] When you get the result, there will be a link for showing that result in [[FirstGlance in Jmol]]. FirstGlance has many conveniences and advantages over other viewers.
+If, in Proteopedia, the molecule of interest has no ''Evolutionary Conservation'' Section, calculate the conservation pattern yourself at the ConSurf Server. [[Quick ConSurf Analysis Procedure|Here are instructions.]] When you get the result, there will be a link for showing that result in [[FirstGlance in Jmol]]. FirstGlance has [[#Conservation in FirstGlance|many conveniences and advantages]] over other viewers.
 ==Conservation in Green Links in Proteopedia==
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 ==Conservation in FirstGlance==
-Exploring conservation in [[FirstGlance in Jmol|FirstGlance]] has many advantages. You can easily hide portions of the molecule, locate sequence numbers of interest, examine the conservation of the amino acids that bind a ligand, etc. See this [http://firstglance.jmol.org/notes.htm#consurffg List of Advantages].
+Exploring conservation in [[FirstGlance in Jmol|FirstGlance]] has many advantages. You can easily hide portions of the molecule, locate sequence numbers of interest, examine the conservation of the amino acids that bind a ligand, etc. See this [http://firstglance.jmol.org/notes.htm#consurffg List of Advantages]. In order to visualize/analyze your ConSurf result in FirstGlance, you must process your PDB file at the ConSurf Server following [[Quick ConSurf Analysis Procedure|these instructions]]. Unfortunately, PDB files from the ConSurf Database (ConSurfDB) had their interface to FirstGlance removed in 2022, so these PDB files no longer work in FirstGlance.
-*Enter your [[PDB code]] at [http://consurfdb.tau.ac.il the ConSurf Database (ConSurfDB)]. In some cases, once you choose a single protein chain, there will be a link to view a pre-calculated evolutionary conservation pattern in FirstGlance.
+You can only color one chain at a time by evolutionary conservation when using FirstGlance. [[Conservation%2C_Evolutionary#Use_Caution_When_Comparing_Conservation_of_Sequence-Different_Chains|Here is the reason.]]
-* If not, you will need to calculate the evolutionary conservation pattern following [[Quick ConSurf Analysis Procedure|these instructions]].
+==See Also==
+*[[ConSurf/Index]], a list of all articles in Proteopedia providing guidance to using ConSurf.
-You can only color one chain at a time by evolutionary conservation when using FirstGlance. [[Conservation%2C_Evolutionary#Use_Caution_When_Comparing_Conservation_of_Sequence-Different_Chains|Here is the reason.]]