How to predict structures with AlphaFold: Difference between revisions

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Eric Martz (talk | contribs)
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[http://firstglance.jmol.org FirstGlance in Jmol] automatically colors its initial view of uploaded AlphaFold or RoseTTAFold models by estimated confidence [[pLDDT]] ('''{{Font color|blue|blue for high confidence}}, {{Font color|red|red for low confidence}}'''). After you go to other views or tools, you can always get back to this color scheme by clicking ''Reliability Estimates'' in the ''Views'' tab.
[http://firstglance.jmol.org FirstGlance in Jmol] automatically colors its initial view of AlphaFold or RoseTTAFold models by estimated confidence [[pLDDT]] ('''{{Font color|blue|blue for high confidence}}, {{Font color|red|red for low confidence}}'''). After you go to other views or tools, you can always get back to this color scheme by clicking ''Reliability Estimates'' in the ''Views'' tab.


*[[iCn3D]] automatically colors AlphaFold2 Database models loaded from their UniProt IDs. For AlphaFold files opened from your computer, use pLDDT on the pull-down Color menu.
*[[iCn3D]] automatically colors AlphaFold2 Database models loaded from their UniProt IDs. For AlphaFold files opened from your computer, use pLDDT on the pull-down Color menu.
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[http://firstglance.jmol.org/where.htm#uploading Upload] your predicted PDB file to [http://firstglance.jmol.org FirstGlance.Jmol.Org], which has many [http://firstglance.jmol.org/whatis.htm#unique unique conveniences and capabilities].
[http://firstglance.jmol.org/where.htm#uploading Upload] your predicted PDB file to [http://firstglance.jmol.org FirstGlance.Jmol.Org], which has many [http://firstglance.jmol.org/whatis.htm#unique unique conveniences and capabilities].


You can easily visualize
When using [http://FirstGlance.jmol.org FirstGlance], it is easy to visualize
* Estimated confidence/pLDDT by touching an atom
* Estimated confidence/pLDDT by touching an atom
* '''Average confidence/pLDDT''' ("reliability") for the entire model, or for [[FirstGlance/How to get average pLDDT from AlphaFold models|a specified sequence range]].
* '''Average confidence/pLDDT''' ("reliability") for the entire model, or for [[FirstGlance/How to get average pLDDT from AlphaFold models|a specified sequence range]].
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