ConSurf Quick Analysis Procedure: Difference between revisions
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<li>Enter a job title, which should include the [[PDB code]] or protein name. | <li>Enter a job title, which should include the [[PDB code]] or protein name. | ||
<li> Enter your email address. | <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]]), you can click <i>Select run parameters manually</i> to try improving the result. | <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''. | <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> | </ol> | ||
'''Why ''FirstGlance in Jmol''?''' Because 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]]. | '''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]]. | ||
Want to make sure your ConSurf result is optimal for answering your questions? See [[Interpreting ConSurf Results]]. | Want to make sure your ConSurf result is optimal for answering your questions? See [[Interpreting ConSurf Results]]. | ||
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* '''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. | * '''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. | ||
==See Also== | |||
*[[ConSurf/Index]] | |||
