FirstGlance/Virus Capsids and Other Large Assemblies: Difference between revisions
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Virus capsids and similarly large protein assemblies can be conveniently visualized and analyzed with [[FirstGlance in Jmol]]. Below some examples are explained and illustrated, but here is a '''quick start''': [http://bioinformatics.org/firstglance/fgij4/fg.htm?mol=1pov polio virus capsid in FirstGlance] ([[1pov]]). | Virus capsids and similarly large protein assemblies can be conveniently visualized and analyzed with [[FirstGlance in Jmol]]. Below some examples are explained and illustrated, but here is a '''quick start''': [http://bioinformatics.org/firstglance/fgij4/fg.htm?mol=1pov polio virus capsid in FirstGlance] ([[1pov]]). | ||
FirstGlance in Jmol automatically constructs [[biological unit]] 1, thought to be the major functional quaternary assembly. Biological unit 1 is shown initially by default, and you can start separate sessions to show the [[asymmetric unit]] or other biological units when more than one are specified. When the resulting assembly is too large to work smoothly and efficiently in FirstGlance in Jmol (all Javascript), FirstGlance will [http://bioinformatics.org/firstglance/fgij4/notes.htm#simplification automatically simplify the model] to alpha carbons, or when necessary, to a subset of alpha carbons. | FirstGlance in Jmol automatically constructs [[biological unit]] 1, thought to be the major functional quaternary assembly. [http://bioinformatics.org/firstglance/fgij4/notes.htm#bu Biological unit 1 is shown initially by default], and you can start separate sessions to show the [[asymmetric unit]] or other biological units when more than one are specified. When the resulting assembly is too large to work smoothly and efficiently in FirstGlance in Jmol (all Javascript), FirstGlance will [http://bioinformatics.org/firstglance/fgij4/notes.htm#simplification automatically simplify the model] to alpha carbons, or when necessary, to a subset of alpha carbons. | ||
Most of the scenes below use color schemes that are built into FirstGlance, and are displayed very easily with just a few clicks of the mouse. The evolutionary conservation color scheme requires that the model be pre-processed by the [[ConSurf/Index|ConSurf Server]]. It produces a PDB file understood by FirstGlance, which will automatically color the model by evolutionary conservation in its initial view. | Most of the scenes below use color schemes that are built into FirstGlance, and are displayed very easily with just a few clicks of the mouse. The evolutionary conservation color scheme requires that the model be pre-processed by the [[ConSurf/Index|ConSurf Server]]. It produces a PDB file understood by FirstGlance, which will automatically color the model by evolutionary conservation in its initial view. | ||