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 | [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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*[[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]]. | *[[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. If your does not, please see the instructions [[#My Molecule Has No Evolutionary Conservation Section in Proteopedia|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'' Section in Proteopedia== | ==My Molecule Has No ''Evolutionary Conservation'' Section in Proteopedia== | ||
If, in Proteopedia, the molecule of interest has no ''Evolutionary Conservation'' Section | 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== | ||
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.]] | |||
==See Also== | |||
*[[ConSurf/Index]], a list of all articles in Proteopedia providing guidance to using ConSurf. | |||