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]] | 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> | <ol> | ||
<li> Go to the [http://consurf.tau.ac.il ConSurf Server]. | <li> Go to the [http://consurf.tau.ac.il ConSurf Server]. | ||
<li> Enter your [[PDB code]] (or upload your [[Atomic coordinate file|PDB file]]). | |||
<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]]) | [[FirstGlance in Jmol]].) | ||
<li> Choose one chain from the pull-down '' | <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> | ||
[[FirstGlance in Jmol]]. | <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''. | |||
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<li> | |||
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<li> Processing may take a few minutes or a few hours. After <font color=" | |||
</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]]. | ||
'''Two methods for viewing your results in FirstGlance:''' | |||
* | * 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. | ||
* '''Right''' click the link ''PDB File | * '''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. | ||
Latest revision as of 22:33, 18 August 2024
Updated 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.)
- 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 analyze only 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 and Limiting ConSurf Analysis to Proteins of a Single Function), 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 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.
Two methods for viewing your results in FirstGlance:
- 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 FirstGlance.Jmol.Org, proceed to upload the downloaded file.
- Right click the link Download ConSurf PDB File for FirstGlance in Jmol, and select Copy Link. Then at 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.