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How to see conserved regions: Difference between revisions

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==Conservation in Proteopedia==
==Conservation in Proteopedia==


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


Most molecules in Proteopedia, on pages titled with a [[PDB code]], have an ''Evolutionary Conservation'' line below the molecule. Clicking on '''<nowiki>[show]</nowiki>''' in this line will color the molecule by evolutionary conservation, as calculated by [[ConSurfDB_vs._ConSurf|ConSurfDB]].
*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).


If the molecule of interest lacks the ''Evolutionary Conservation'' line below the molecule, please see the instructions [[#My Molecule Has No Evolutionary Conservation Line|below]].
*[[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, 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==
==Conservation in Green Links in Proteopedia==
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==Conservation in FirstGlance==
==Conservation in FirstGlance==


You might wish to explore a conservation-colored molecule in [[FirstGlance in Jmol|FirstGlance]] so you can hide portions of it, locate sequence numbers of interest, or examine the conservation of the amino acids that bind a ligand, or for other reasons.
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 the [[PDB code]] in the search slot in Proteopedia.
#At the page title with the PDB code, click on '''<nowiki>[show]</nowiki>''' in the line labeled ''Evolutionary Conservation'' beneath the molecule. (If there is no such line, see below.)
#The ''Evolutionary Conservation'' section is now expanded. Click on the link ''Complete Results at ConSurfDB''.
#At ConSurfDB, click on the button for the chain of interest under ''View 3D structure colored by conservation in FirstGlance in Jmol''. (You can only see one chain at a time at ConSurfDB. [[Conservation%2C_Evolutionary#Use_Caution_When_Comparing_Conservation_of_Sequence-Different_Chains|Here is the reason.]])
 
==My Molecule Has No Evolutionary Conservation Line==


If, in Proteopedia, the molecule of interest lacks the ''Evolutionary Conservation'' line below the molecule:
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.]]


#Try looking directly in [[http://consurfdb.tau.ac.il ConSurfDB] which is self-explanatory. If there are no results there for your molecule, or if you wish to obtain better results, try the next step.
==See Also==
#Calculate the conservation pattern yourself at the ConSurf Server. [[ConSurfDB_vs._ConSurf#Limiting_ConSurf_Analysis_to_Proteins_of_a_Single_Function|Here are instructions.]] When you get the result, there will be a link for showing that result in [[FirstGlance in Jmol]].
*[[ConSurf/Index]], a list of all articles in Proteopedia providing guidance to using ConSurf.

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