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FirstGlance/Index
From Proteopedia
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*[[FirstGlance in Jmol]] - Overview of the software package and its integration into Proteopedia. | *[[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. | *[[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. | *[[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. | *[[Biological Unit]] tells how to visualize the biological unit in FirstGlance. | ||
*[[Cation-pi interactions]] mentions that FirstGlance has a tool to display these easily. | *[[Cation-pi interactions]] mentions that FirstGlance has a tool to display these easily. | ||
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*[[Disulfide bond]] mentions FirstGlance's tool that highlights these and quantitates all sulfurs and seleniums. | *[[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. | *[[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/Evaluating Protein Crosslinks]] [[Image:New yellow1.gif]] | ||
*[[FirstGlance/How To Measure A Virus Capsid]] [[Image:New yellow1.gif]] | *[[FirstGlance/How To Measure A Virus Capsid]] [[Image:New yellow1.gif]] | ||
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*[http://firstglance.jmol.org FirstGlance.Jmol.Org]: the software package itself. | *[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/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/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://tinyurl.com/movingmolecules tinyurl.com/movingmolecules]: Examples (in Google Slides) of animations easily created in FirstGlance. | ||
Current revision
A list of pages and resources related to FirstGlance in Jmol:
Proteopedia Pages
- 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.
- 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 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
mentions how easy it is to see them in FirstGlance, and provides animated illustrations from FirstGlance.
- Electrostatic potential maps
- FirstGlance/Evaluating Protein Crosslinks
- FirstGlance/How To Measure A Virus Capsid
- FirstGlance/Visualizing Conservation: Easy ways to see 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 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.
- 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
- FirstGlance.Jmol.Org: the software package itself.
- What Is FirstGlance in Jmol: an overview of capabilities.
- Design of FirstGlance in Jmol, and its Forerunners
- tinyurl.com/firstglance1: YouTube illustrated talk introducing FirstGlance and its design goals.
- tinyurl.com/movingmolecules: Examples (in Google Slides) of animations easily created in FirstGlance.
- Index to FirstGlance: Where to find specific tools within FirstGlance, and how to do specific tasks using FirstGlance.
