ConSurf Quick Analysis Procedure: Difference between revisions

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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. If you wish to take it further, see [[ConSurfDB_vs._ConSurf#Limiting_ConSurf_Analysis_to_Proteins_of_a_Single_Function|Limiting ConSurf Analysis to Proteins of a Single Function]].
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. If you wish to take it further, see [[ConSurfDB_vs._ConSurf#Limiting_ConSurf_Analysis_to_Proteins_of_a_Single_Function|Limiting ConSurf Analysis to Proteins of a Single Function]].


# Go to the [http://consurf.tau.ac.il ConSurf Server].
<ol>
# Check ''Amino Acids''.
<li> Go to the [http://consurf.tau.ac.il ConSurf Server].
# Check '''Yes''' there is a known protein structure.
<li> Check ''Amino Acids''.
# Enter your [[PDB code]] and click the ''Next'' button.
<li> Check '''Yes''' there is a known protein structure.
# 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]].)
<li> Enter your [[PDB code]] and click the ''Next'' button.
# Check '''No''' you do not have a Multiple Sequence Alignment (MSA) to upload.
<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]].)
# Don't worry, you can leave all the settings that appear now at their defaults.<blockquote>If you want the server to return your result faster, reduce ''Maximum homologs to collect'' from 150 to 75.</blockquote>
<br><br>
# '''Enter your email address''' in the bottom slot! This avoids losing the result and having to do it over.
 
 
<li> Check '''No''' you do not have a Multiple Sequence Alignment (MSA) to upload.
<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.
<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.
<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''',
</ol>
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