FirstGlance/Index: Difference between revisions

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A list of pages and resources related to [[FirstGlance in Jmol]]:

~~'''~~Proteopedia Pages~~'''~~

==Proteopedia Pages==

*[[FirstGlance in Jmol]] - Overview of the software package.

*[[FirstGlance in Jmol]] - Overview of the software package and its integration into Proteopedia.

*[[FirstGlance in Jmol Literature Citations]] lists some of the recent scientific journal publications where it was utilized and cited.

*[[FirstGlance/Virus Capsids and Other Large Assemblies]] New capabilities in August, 2022.

*[[How to predict structures with AlphaFold|AlphaFold: How to predict structures]] has a section on the advantages of visualization of predicted structures in FirstGlance.

*AlphaFold: [[FirstGlance/How to get average pLDDT from AlphaFold models]].

*AlphaFold3: [[Converting_AlphaFold3_CIF_to_PDB|Converting AlphaFold3 CIF models to PDB for use in FirstGlance]].

*[[Biological Unit]] tells how to visualize the biological unit in FirstGlance.

*[[Cation-pi interactions]] mentions that FirstGlance has a tool to display these easily.

*[[ConSurf Quick Analysis Procedure]] mentions using FirstGlance to visualize ConSurf results.

*[[Disulfide bond]] mentions FirstGlance's tool that highlights these and quantitates all sulfurs and seleniums.

*[[Electron density maps]] [[Image:New yellow1.gif]] mentions how easy it is to see them in FirstGlance, and provides animated illustrations from FirstGlance.

*[[Electrostatic potential maps]] [[Image:New yellow1.gif]]

*[[FirstGlance/Evaluating Protein Crosslinks]] [[Image:New yellow1.gif]]

*[[FirstGlance/How To Measure A Virus Capsid]] [[Image:New yellow1.gif]]

*[[FirstGlance/Visualizing Conservation]]: [[Image:New yellow1.gif]] Easy ways to see [[ConSurf/Index|ConSurf]] colors for residues of interest.

*[[Free R]] tells how FirstGlance helps to interpret free R.

*[[Help:Copying FirstGlance Scenes into Proteopedia]]

*[[Hydrogen bonds]] describes the ''Contacts & Non-Covalent Interactions'' tool in FirstGlance.

*[[How to see conserved regions]] includes a section on FirstGlance.

*[[Interpreting ConSurf Results]] [[Image:New yellow1.gif]] discusses advantages of using FirstGlance.

*[[Practical Guide to Homology Modeling]] a section on visualizing predicted structures in FirstGlance.

*[[Protein crosslinks]]: FirstGlance automatically detects and alerts you to six unusual types.

*[[Salt bridges]] mentions that FirstGlance has a tool to display these easily.

*[[User:Eric Martz/Introduction to Structural Bioinformatics|Introduction to Structural Bioinformatics]]: Syllabi and assessment tools based heavily on use of FirstGlance by students.

*[[Temperature value]] mentions the use of FirstGlance to color by temperature, and to list missing residues and incomplete sidechains.

==External Resources==

*[http://firstglance.jmol.org FirstGlance.Jmol.Org]: the software package itself.

*[http://firstglance.jmol.org/whatis.htm What Is FirstGlance in Jmol]: an overview of capabilities.

*[http://firstglance.jmol.org/design.htm Design of FirstGlance in Jmol, and its Forerunners]

*[http://tinyurl.com/firstglance1 tinyurl.com/firstglance1]: YouTube illustrated talk introducing FirstGlance and its design goals.

*[http://tinyurl.com/movingmolecules tinyurl.com/movingmolecules]: Examples (in Google Slides) of animations easily created in FirstGlance.

*[http://firstglance.jmol.org/where.htm Index to FirstGlance]: Where to find specific tools within FirstGlance, and how to do specific tasks using FirstGlance.

==See Also==

*[[Jmol/Index]]

*[[ConSurf/Index]]

*[[Index pages]]

FirstGlance/Index: Difference between revisions

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@@ Line 1: / Line 1: @@
 A list of pages and resources related to [[FirstGlance in Jmol]]:
-'''Proteopedia Pages'''
+==Proteopedia Pages==
-*[[FirstGlance in Jmol]] - Overview of the software package.
+*[[FirstGlance in Jmol]] - Overview of the software package and its integration into Proteopedia.
+*[[FirstGlance in Jmol Literature Citations]] lists some of the recent scientific journal publications where it was utilized and cited.
+*[[FirstGlance/Virus Capsids and Other Large Assemblies]] New capabilities in August, 2022.
+*[[How to predict structures with AlphaFold|AlphaFold: How to predict structures]] has a section on the advantages of visualization of predicted structures in FirstGlance.
+*AlphaFold: [[FirstGlance/How to get average pLDDT from AlphaFold models]].
+*AlphaFold3: [[Converting_AlphaFold3_CIF_to_PDB|Converting AlphaFold3 CIF models to PDB for use in FirstGlance]].
+*[[Biological Unit]] tells how to visualize the biological unit in FirstGlance.
+*[[Cation-pi interactions]] mentions that FirstGlance has a tool to display these easily.
+*[[ConSurf Quick Analysis Procedure]] mentions using FirstGlance to visualize ConSurf results.
+*[[Disulfide bond]] mentions FirstGlance's tool that highlights these and quantitates all sulfurs and seleniums.
+*[[Electron density maps]] [[Image:New yellow1.gif]] mentions how easy it is to see them in FirstGlance, and provides animated illustrations from FirstGlance.
+*[[Electrostatic potential maps]] [[Image:New yellow1.gif]]
+*[[FirstGlance/Evaluating Protein Crosslinks]] [[Image:New yellow1.gif]]
+*[[FirstGlance/How To Measure A Virus Capsid]] [[Image:New yellow1.gif]]
+*[[FirstGlance/Visualizing Conservation]]: [[Image:New yellow1.gif]] Easy ways to see [[ConSurf/Index|ConSurf]] colors for residues of interest.
+*[[Free R]] tells how FirstGlance helps to interpret free R.
+*[[Help:Copying FirstGlance Scenes into Proteopedia]]
+*[[Hydrogen bonds]] describes the ''Contacts & Non-Covalent Interactions'' tool in FirstGlance.
+*[[How to see conserved regions]] includes a section on FirstGlance.
+*[[Interpreting ConSurf Results]] [[Image:New yellow1.gif]] discusses advantages of using FirstGlance.
+*[[Practical Guide to Homology Modeling]] a section on visualizing predicted structures in FirstGlance.
+*[[Protein crosslinks]]: FirstGlance automatically detects and alerts you to six unusual types.
+*[[Salt bridges]] mentions that FirstGlance has a tool to display these easily.
+*[[User:Eric Martz/Introduction to Structural Bioinformatics|Introduction to Structural Bioinformatics]]: Syllabi and assessment tools based heavily on use of FirstGlance by students.
+*[[Temperature value]] mentions the use of FirstGlance to color by temperature, and to list missing residues and incomplete sidechains.
+==External Resources==
+*[http://firstglance.jmol.org FirstGlance.Jmol.Org]: the software package itself.
+*[http://firstglance.jmol.org/whatis.htm What Is FirstGlance in Jmol]: an overview of capabilities.
+*[http://firstglance.jmol.org/design.htm Design of FirstGlance in Jmol, and its Forerunners]
+*[http://tinyurl.com/firstglance1 tinyurl.com/firstglance1]: YouTube illustrated talk introducing FirstGlance and its design goals.
+*[http://tinyurl.com/movingmolecules tinyurl.com/movingmolecules]: Examples (in Google Slides) of animations easily created in FirstGlance.
+*[http://firstglance.jmol.org/where.htm Index to FirstGlance]: Where to find specific tools within FirstGlance, and how to do specific tasks using FirstGlance.
+==See Also==
+*[[Jmol/Index]]
+*[[ConSurf/Index]]
+*[[Index pages]]