View source for How to see conserved regions

Conserved regions on the surface of a folded protein molecule identify functional sites. For an explanation with examples, please see [[Introduction to Evolutionary Conservation]].

==Conservation in Proteopedia==

[http://proteopedia.org/w/How_to_see_conserved_regions Right click here to open a duplicate of this page in a separate tab or window] so you can keep this page visible.

Enter your [[PDB code]] in the ''upper'' search slot at the left side of the either tab/window. This should take you to a page titled with your PDB code, such as [[2hhd]].

*Click the <font color="#e08000">orange '''load full''' button</font> to load all atoms in the model (rather than the initial simplified model, which loads only alpha carbon atoms).

*[[Image:Evolutionary conservation section.png|border|right|300px]]Look for the section ''Evolutionary Conservation'' and check a checkbox there to color the molecule according to [[ConSurfDB_vs._ConSurf|ConSurfDB]].

Not all pages titled with a PDB code have an ''Evolutionary Conservation'' section (example: [[4d7b]]). If your does not, please see the instructions [[#My Molecule Has No Evolutionary Conservation Section in Proteopedia|below]].

==My Molecule Has No ''Evolutionary Conservation'' Section in Proteopedia==

If, in Proteopedia, the molecule of interest has no ''Evolutionary Conservation'' Section:

#Try looking directly in [http://consurfdb.tau.ac.il ConSurfDB]. If it has no results for your molecule, or if you wish to obtain better results, try the next step.
#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]].

==Conservation in Green Links in Proteopedia==

You can [[Help:How to Insert a ConSurf Result Into a Proteopedia Green Link|show ConSurf-colored molecules with green links in Proteopedia]].

==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].

*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.]]