ConSurf Quick Analysis Procedure: Difference between revisions
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<li>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]]. | <li>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. | ||
<li> | <li>Enter a job title, which should include the [[PDB code]] or protein name. | ||
<li> | <li> Enter your email address. | ||
<li> | <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> 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''. | ||
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<li> Processing may take a few minutes or a few hours. After <font color=" | |||
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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]]. | ||
* At the ConSurf results page, click ''PDB File with ConSurf Results in its Header, for FirstGlance in Jmol'' to download the PDB file. Then at [http://firstglance.jmol.org FirstGlance.Jmol.Org], upload the downloaded file. | * At the ConSurf results page, click ''PDB File with ConSurf Results in its Header, for FirstGlance in Jmol'' to download the PDB file. Then at [http://firstglance.jmol.org FirstGlance.Jmol.Org], upload the downloaded file. | ||
* '''Right''' click the link ''PDB File with ConSurf Results in its Header, for FirstGlance in Jmol'', and select Copy Link. Then at [http://firstglance.jmol.org FirstGlance.Jmol.Org], click ''enter a molecule's URL'' and past 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 ''PDB File with ConSurf Results in its Header, for FirstGlance in Jmol'', and select Copy Link. Then at [http://firstglance.jmol.org FirstGlance.Jmol.Org], click ''enter a molecule's URL'' and past 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. | ||
Revision as of 00:08, 4 July 2024
Here is a quick procedure for coloring a protein molecule by evolutionary conservation. (This page is a supplement to How to see conserved regions. This page was updated in July, 2024.)
- Go to the ConSurf Server.
- Enter your PDB code (or upload your PDB file).
- Choose one chain from the pull-down Select chain identifier menu. (ConSurf can only analyze one chain at a time. Get chain IDs by examining the model in
FirstGlance in Jmol.
- You will likely be offered a pre-calculated result in the ConSurf DataBase ConSurfDB, but it cannot be used in FirstGlance in Jmol, which has many powerful conveniences for visualizing conservation patterns. Continue with the steps below to get a FirstGlance-compatible result.
- Enter a job title, which should include the PDB code or protein name.
- Enter your email address.
- If this is your first try with this protein, click Submit with default parameters. If the default result needs improvement (see Interpreting ConSurf Results), you can click Select run parameters manually to try improving the result.
- Processing may take a few minutes or a few hours. After FINISHED appears at the top of the ConSurf Job Status Page, click Go To The Results.
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.
Want to make sure your ConSurf result is optimal for answering your questions? See Interpreting ConSurf Results.
- At the ConSurf results page, click PDB File with ConSurf Results in its Header, for FirstGlance in Jmol to download the PDB file. Then at FirstGlance.Jmol.Org, upload the downloaded file.
- Right click the link PDB File with ConSurf Results in its Header, for FirstGlance in Jmol, and select Copy Link. Then at FirstGlance.Jmol.Org, click enter a molecule's URL and past 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.