How to see conserved regions: Difference between revisions

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Eric Martz

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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.
-* If not, you will need to calculate the evolutionary conservation pattern following [[Quick ConSurf Analysis Procedure|these instructions]].
 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.]]