ConSurf Quick Analysis Procedure: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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-Here is a quick procedure for coloring a protein molecule by [[Introduction to Evolutionary Conservation|evolutionary conservation]]. This procedure does not necessarily give the highest quality result, but will give you a preliminary result that is often sufficient. (This page is a supplement to [[How to see conserved regions]].)
+Updated ''July, 2024''.
+'''Here is a quick procedure''' for coloring a protein molecule by [[Introduction to Evolutionary Conservation|evolutionary conservation]]. (This page is a supplement to [[How to see conserved regions]].)
 <ol>
 <li> Go to the [http://consurf.tau.ac.il ConSurf Server].
-<li> Check ''Amino Acids''.
+<li> Enter your [[PDB code]] (or upload your [[Atomic coordinate file|PDB file]]).
-<li> Check '''Yes''' there is a known protein structure.
+<li> Choose one chain from the pull-down ''Select chain identifier'' menu. (ConSurf can analyze only [[Conservation%2C_Evolutionary#Use_Caution_When_Comparing_Conservation_of_Sequence-Different_Chains|one chain at a time]]. Get chain IDs by examining the model in
-<li> Enter your [[PDB code]] (or upload your [[Atomic coordinate file|PDB file]]) and click the ''Next'' button.
+[[FirstGlance in Jmol]].)
-<li> Choose one chain from the pull-down ''Chain Identifier'' menu. (ConSurf can only analyze [[Conservation%2C_Evolutionary#Use_Caution_When_Comparing_Conservation_of_Sequence-Different_Chains|one chain at a time]].)
+<ul>You will likely be offered a pre-calculated result in the ConSurf DataBase <i>ConSurf<b>DB</b></i>, but it cannot be used in [[FirstGlance in Jmol]], which has many powerful conveniences for [[FirstGlance/Visualizing Conservation|visualizing conservation patterns]]. Continue with the steps below to get a FirstGlance-compatible result.</ul>
-<br><br>
+<li>Enter a job title, which should include the [[PDB code]] or protein name.
+<li> Enter your email address.
+<li> If this is your first try with this protein, click <i>Submit with default parameters</i>. If the default result needs improvement (see [[Interpreting ConSurf Results]] and [[ConSurfDB_vs._ConSurf#Limiting_ConSurf_Analysis_to_Proteins_of_a_Single_Function|Limiting ConSurf Analysis to Proteins of a Single Function]]), you can click <i>Select run parameters manually</i> to try improving the result.
+<li> Processing may take a few minutes or a few hours. After <font color="#00b000">FINISHED</font> appears at the top of the ''ConSurf Job Status Page'', click ''Go To The Results''.
+</ol>
+'''Why ''FirstGlance in Jmol''?''' Because it has [http://firstglance.jmol.org/notes.htm#consurffg many advantages]. It has shortcut tools making it easy to see conservation of salt bridges, cation-pi interactions, the residues binding ligands/substrates/inhibitors, the residues engaging in [[protein crosslinks]], or any residues that you specify. For a tour of these tools, see [[FirstGlance/Visualizing Conservation]].
-<li> Check '''No''' you do not have a Multiple Sequence Alignment (MSA) to upload.
+Want to make sure your ConSurf result is optimal for answering your questions? See [[Interpreting ConSurf Results]].
-<li> Don't worry, you can leave all the settings that appear now at their defaults.
-:If you want the server to return your result faster, reduce ''Maximum homologs to collect'' from 150 to 75.
+'''Two methods for viewing your results in FirstGlance:'''
-<li> '''Enter your email address''' in the bottom slot! This avoids losing the result and having to do it over.
-<li> Click the ''Submit'' button.
+* At the ConSurf results page, open ''High Resolution Figures and PDB Files'', and then click ''Download ConSurf PDB File for FirstGlance in Jmol''. Then at [http://firstglance.jmol.org FirstGlance.Jmol.Org], proceed to [http://firstglance.jmol.org/where.htm#uploading upload] the downloaded file.
-<li> Processing may take a few minutes or a few hours. After <font color="red">FINISHED</font> appears at the top of the '''Job Status Page''', scroll down to ''Final Results'' and click ''View ConSurf Results with FirstGlance in Jmol''.
-</ol>
-If you want to obtain a better quality result, see [[ConSurfDB_vs._ConSurf#Limiting_ConSurf_Analysis_to_Proteins_of_a_Single_Function|Limiting ConSurf Analysis to Proteins of a Single Function]].
+* '''Right''' click the link ''Download ConSurf PDB File for FirstGlance in Jmol'', and select Copy Link. Then at [http://firstglance.jmol.org FirstGlance.Jmol.Org], click ''enter a molecule's URL'' and paste the link into the slot. This requires that the ConSurf job be recent, since the results will remain on the server for a limited time.