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| + | == Notes == | ||
| + | Each major link should link to a category page. Then, each category page should have a short intro and the auto-generated out-going links to each of its pages. This way, we get coverage with minimal effort. | ||
| + | == New Table == | ||
| + | Here's the code for a new table for this page. This page is quite popular and needs to be cleaned up...alot. Feel free to make changes to the main TOPTOC as needed. | ||
| + | {| style="border: align:center; width:100%; background:#E5DBCF; border: 3px solid #333;" | ||
| + | |- | ||
| + | | align="left" valign="top" | | ||
| + | {| style="color:#CC9752; padding: 10px; background: transparent;" | ||
| + | ! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left;" colspan="2" | Installation, Configuration & Learning | ||
| + | |- | ||
| + | | style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"| | ||
| + | # '''[[:Category:Installation|Installation]]''' | ||
| + | ## [[Linux_Install|Linux]] | ||
| + | ## [[MAC_Install|MAC]] | ||
| + | ## [[Windows_Install|Windows]] | ||
| + | # '''[[:Category:Stereo 3D Display|Stereo 3D Display]]''' | ||
| + | ## [[Linux XFree86 Configuration]] | ||
| + | [[Image:0903_1_1.jpg|center|85px]] | ||
| + | | style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"| | ||
| + | # '''[[:Category:Using Pymol|Using PyMol]]''' | ||
| + | ## '''[[:Category:Launching|Launching]]''' | ||
| + | ### [[Launching PyMOL|Launching PyMOL]] | ||
| + | ### [[Command_Line_Options|Command Line Options]] | ||
| + | ### [[Launching_From_a_Script|Launching From a Script]] | ||
| + | ## [[Mouse_Controls|Mouse Controls]] | ||
| + | ## '''[[:Category:Objects and Selections|Objects and Selections]]''' | ||
| + | ### '''[[:Category:Working with Objects|Working with Objects]]''' | ||
| + | ### '''[[:Category:Working with Selections|Working with Selections]]''' | ||
| + | ### '''[[:Category:Selector_Quick_Reference|Selector Quick Reference]]''' | ||
| + | #### [[Single-word Selectors|Single-word Selectors]] | ||
| + | #### [[Property Selectors|Property Selectors]] | ||
| + | #### [[Selection Algebra|Selection Algebra]] | ||
| + | #### [[Selection Macros|Selection Macros]] | ||
| + | |} | ||
| + | | align="left" valign="top" | | ||
| + | {| style="color:#CC9752; padding: 10px; background: transparent;" | ||
| + | !style="background:transparent; font-size: 150%; text-decoration:underline; vertical-align:top; text-align:left;" colspan="2" | Commands, Representations & Settings | ||
| + | |- | ||
| + | | style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"| | ||
| + | # '''[[:Category:Commands|PyMOL Commands]]''' | ||
| + | # '''[[:Category:Settings|Settings (Documented)]]''' | ||
| + | ## [[Settings|All]] | ||
| + | [[Image:050429science.pdf.jpg|85px|center]] | ||
| + | | style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"| | ||
| + | # '''[[:Category:Representations|Representations]]''' | ||
| + | ## [[Lines|Lines]] | ||
| + | ## [[Sticks|Sticks]] | ||
| + | ## [[Ball_and_Stick|Ball and Sticks]] | ||
| + | ## [[Cartoon|Cartoon]] | ||
| + | ## [[Surface|Surface]] | ||
| + | ## [[Mesh|Mesh]] | ||
| + | ## [[Spheres|Spheres]] | ||
| + | ## [[Dots|Dots]] | ||
| + | # '''[[:Category:Coloring|Coloring]]''' | ||
| + | ## [[Color|Color]] | ||
| + | |} | ||
| + | |- | ||
| + | | align="left" valign="top" | | ||
| + | {| style="color:#CC9752; padding: 10px; background: transparent;" | ||
| + | ! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left;" colspan="2" | Physico-chemical Modeling | ||
| + | |- | ||
| + | | style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"| | ||
| + | # '''[[:Category:Biochemical_Properties|Biochemical Properties]]''' | ||
| + | ## [[Displaying Biochemical Properties|Displaying biochemical properties]] | ||
| + | ## [[Surfaces_and_Voids|Surfaces and Voids]] | ||
| + | [[Image:Ribbon_hh1.png|center|85px]] | ||
| + | | style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"| | ||
| + | # [[Modeling_and_Editing_Structures|Modeling and editing structures]] | ||
| + | ## [[Editing atoms|Editing Atoms]] | ||
| + | ## [[Molecular Sculpting|Molecular sculpting]] | ||
| + | ## [[Homology Modeling|Homology modeling]] | ||
| + | |} | ||
| + | | align="left" valign="top" | | ||
| + | {| style="color:#CC9752; padding: 10px; background: transparent;" | ||
| + | ! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left; vertical-align:top;" colspan="2" | Images & Movies | ||
| + | |- | ||
| + | | style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"| | ||
| + | # '''[[:Category:Image Manipulation|Image Manipulation]]''' | ||
| + | ## [[Label|Labels]] | ||
| + | ## Photoshop/GIMP | ||
| + | ## [[Stereo_Ray|Stereo Figures]] | ||
| + | ## [[Publication Quality Images|Publication-quality images]] | ||
| + | ## [[PovRay|PovRay]] | ||
| + | | | ||
| + | | style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"| | ||
| + | # [[Making_Movies|Making Movies]] | ||
| + | ## [[Software_Codecs|Codecs]] | ||
| + | [[Image:070816nature.pdf.jpg|center|85px]] | ||
| + | |} | ||
| + | |- | ||
| + | | align="left" valign="top" | | ||
| + | {| style="color:#CC9752; padding: 10px; background: transparent;" | ||
| + | ! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left;" colspan="2" | Extending, Embedding & Scripting | ||
| + | |- | ||
| + | | style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"| | ||
| + | # [[Scripting|Scripting]] | ||
| + | ## [[Example Scripts|Example Scripts]] | ||
| + | ## '''[[:Category:Script Library|Script Library]]''' | ||
| + | # '''[[:Category:Plugins|Plugins]]''' | ||
| + | ## '''[[:Category:Electrostatics|Electrostatics and energy minimization.]]''' | ||
| + | ### [[APBS|APBS Plugin]] | ||
| + | ### [[Protein_contact_potential]] | ||
| + | ## [http://www.rubor.de/bioinf/pymol_extensions.html rtools] | ||
| + | ## [[Plugins_Tutorial|Tutorial on writing plugins]] | ||
| + | ## '''[[:Category:Plugins Others| Others]]''' | ||
| + | | | ||
| + | | style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"| | ||
| + | # High-Level Applications | ||
| + | ## Crystallography Applications | ||
| + | ### Symmetry|Symmetry | ||
| + | ### Electron Density | ||
| + | ## NMR Applications | ||
| + | ### Working with Structure Families | ||
| + | ## '''[[:Category:Structure_Alignment|Superimposition and RMSD]]''' | ||
| + | ### NMR Restraints and Analysis | ||
| + | |} | ||
| + | | align="left" valign="top" | | ||
| + | {| style="color:#CC9752; padding: 10px; background: transparent;" | ||
| + | ! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left; vertical-align:top;" colspan="2"| Third Party Applications | ||
| + | |- | ||
| + | | style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"| | ||
| + | # [[O]] | ||
| + | # [[SURFNET]] | ||
| − | + | [[Image:080602cnen.pdf.jpg|center|85px]] | |
| − | + | | | |
| − | + | | style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"| | |
| − | + | # [[Python_Integration|Python Integration]] | |
| − | + | # '''[[:Category:PyMol_Integration|PyMol_Integration]]''' | |
| − | + | ## [[Nuccyl|Nuccyl]] -- Nuccyl is a great PyMol extension | |
| − | + | ## [[CASTp|CASTp]] -- Binding and Active site prediction | |
| − | + | ## [[CCTBX|CCTBX]] -- Computational Crystallography Toolbox | |
| − | + | ## [[ProMOL]] | |
| − | + | ## [[S2S]] | |
| − | + | ## '''[[:Category:PyMol_Integration Arbitrary_Graphics_Objects|Arbitrary_Graphics_Objects]]''' | |
| − | + | |} | |
| − | + | |} | |
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Latest revision as of 00:44, 28 March 2014
Notes
Each major link should link to a category page. Then, each category page should have a short intro and the auto-generated out-going links to each of its pages. This way, we get coverage with minimal effort.
New Table
Here's the code for a new table for this page. This page is quite popular and needs to be cleaned up...alot. Feel free to make changes to the main TOPTOC as needed.
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