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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, such as [[2hhd]].
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]].
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*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).
*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).
*Look for the section ''Evolutionary Conservation'' and check a checkbox there to color the molecule according to [[ConSurfDB_vs._ConSurf|ConSurfDB]].
*[[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]].
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]].
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'' Line in Proteopedia==
==My Molecule Has No ''Evolutionary Conservation'' Section in Proteopedia==
If, in Proteopedia, the molecule of interest lacks the ''Evolutionary Conservation'' line below the molecule:
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.
#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. [[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]].
==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.
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.]]
#Enter the [[PDB code]] in the search slot in Proteopedia.
==See Also==
#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.)
*[[ConSurf/Index]], a list of all articles in Proteopedia providing guidance to using ConSurf.
#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.]])
Latest revision as of 20:36, 21 July 2024
Conserved regions on the surface of a folded protein molecule identify functional sites. For an explanation with examples, please see Introduction to Evolutionary Conservation.
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 orange load full button to load all atoms in the model (rather than the initial simplified model, which loads only alpha carbon atoms).
Look for the section Evolutionary Conservation and check a checkbox there to color the molecule according to ConSurfDB.
Not all pages titled with a PDB code have an Evolutionary Conservation section (example: 4d7b). If your does not, please see the instructions below.
My Molecule Has No Evolutionary Conservation Section in ProteopediaMy 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. 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.
Conservation in Green Links in ProteopediaConservation in Green Links in Proteopedia
Conservation in FirstGlanceConservation in FirstGlance
Exploring conservation in 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 List of Advantages. In order to visualize/analyze your ConSurf result in FirstGlance, you must process your PDB file at the ConSurf Server following 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.
You can only color one chain at a time by evolutionary conservation when using FirstGlance. Here is the reason.
See AlsoSee Also
ConSurf/Index, a list of all articles in Proteopedia providing guidance to using ConSurf.
Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
