Difference between revisions of "Talk:TOPTOC"

From PyMOLWiki
Jump to navigation Jump to search
Line 3: Line 3:
 
Here's the code for a new table for this page.  This page is quite popular and needs to be cleaned up...alot.
 
Here's the code for a new table for this page.  This page is quite popular and needs to be cleaned up...alot.
  
−
 
+
{| style="border: align:center; width:100%; background:#E5DBCF; border: 3px solid #333;"
−
{| style="border: align:center; width:100%; background:#E5DBCF; border: 1px solid #333;"
 
 
|-
 
|-
−
| align="left" |
+
| align="left" valign="top" |
−
{| style="align:left; color:#CC9752;padding: 10px; text-align:center; background: transparent;"
+
{| style="color:#CC9752; padding: 10px; background: transparent;"
−
! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:center;" colspan=2 | Installation, Configuration & Learning
+
! 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;"|
 
| style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"|
Line 17: Line 16:
 
# '''[[:Category:Stereo 3D Display|Stereo 3D Display]]'''
 
# '''[[:Category:Stereo 3D Display|Stereo 3D Display]]'''
 
## [[Linux XFree86 Configuration]]
 
## [[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;"|
 
| 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:Using Pymol|Using PyMol]]'''
Line 33: Line 35:
 
#### [[Selection Macros|Selection Macros]]
 
#### [[Selection Macros|Selection Macros]]
 
|}
 
|}
−
| align="center" valign="top" |
+
| align="left" valign="top" |
−
{| style="align:left; color:#CC9752; padding: 10px; background: transparent;"
+
{| style="color:#CC9752; padding: 10px; background: transparent;"
−
! colspan="2" style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left; vertical-align:top;" |  Commands, Representations & Settings
+
!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;"|
 
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
Line 41: Line 43:
 
# '''[[:Category:Settings|Settings (Documented)]]'''
 
# '''[[:Category:Settings|Settings (Documented)]]'''
 
## [[Settings|All]]
 
## [[Settings|All]]
 +
 +
 +
[[Image:050429science.pdf.jpg|85px|center]]
 
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
 
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
 
# '''[[:Category:Representations|Representations]]'''
 
# '''[[:Category:Representations|Representations]]'''
Line 55: Line 60:
 
|}
 
|}
 
|-
 
|-
−
| align="center" valign="top" |
+
| align="left" valign="top" |
−
{| style="align:left; color:#CC9752;padding: 10px; text-align:center; background: transparent;"
+
{| style="color:#CC9752; padding: 10px; background: transparent;"
−
! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:center;" colspan=2 | Physico-chemical Modeling
+
! 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;"|
 
| style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"|
Line 63: Line 68:
 
## [[Displaying Biochemical Properties|Displaying biochemical properties]]
 
## [[Displaying Biochemical Properties|Displaying biochemical properties]]
 
## [[Surfaces_and_Voids|Surfaces and Voids]]
 
## [[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;"|
 
| 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]]
 
# [[Modeling_and_Editing_Structures|Modeling and editing structures]]
Line 69: Line 77:
 
## [[Homology Modeling|Homology modeling]]
 
## [[Homology Modeling|Homology modeling]]
 
|}
 
|}
−
| align="center" valign="top" |
+
| align="left" valign="top" |
 
{| style="color:#CC9752; padding: 10px; background: transparent;"
 
{| style="color:#CC9752; padding: 10px; background: transparent;"
−
! colspan="2" style="background:transparent; font-size: 150%; text-decoration:underline; text-align:center; vertical-align:top;" | Images & Movies
+
! 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;"|
 
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
Line 84: Line 92:
 
# [[Making_Movies|Making Movies]]
 
# [[Making_Movies|Making Movies]]
 
## [[Software_Codecs|Codecs]]
 
## [[Software_Codecs|Codecs]]
 +
 +
 +
[[Image:070816nature.pdf.jpg|center|85px]]
 
|}
 
|}
 
|-
 
|-
−
| align="center" valign="top" |
+
| align="left" valign="top" |
−
{| style="align:left; color:#CC9752; padding: 10px; text-align:center; background: transparent;"
+
{| style="color:#CC9752; padding: 10px; background: transparent;"
−
! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:center;" colspan=2 | Extending, Embedding & Scripting
+
! 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;"|
 
| 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;"|
 
| 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="center" valign="top" |
+
| align="left" valign="top" |
−
{| style="align:center; color:#CC9752; padding: 10px; background: transparent;"
+
{| style="color:#CC9752; padding: 10px; background: transparent;"
−
! colspan="2" style="background:transparent; font-size: 150%; text-decoration:underline; text-align:center; vertical-align:top;" |  Third Party Applications
+
! 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;"|
 
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
 
# [[O]]
 
# [[O]]
 
# [[SURFNET]]
 
# [[SURFNET]]
 +
 +
 +
[[Image:080602cnen.pdf.jpg|center|85px]]
 
|
 
|
 
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
 
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|

Revision as of 12:13, 15 September 2008

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.

Installation, Configuration & Learning
  1. Installation
    1. Linux
    2. MAC
    3. Windows
  2. Stereo 3D Display
    1. Linux XFree86 Configuration


0903 1 1.jpg
  1. Using PyMol
    1. Launching
      1. Launching PyMOL
      2. Command Line Options
      3. Launching From a Script
    2. Mouse Controls
    3. Objects and Selections
      1. Working with Objects
      2. Working with Selections
      3. Selector Quick Reference
        1. Single-word Selectors
        2. Property Selectors
        3. Selection Algebra
        4. Selection Macros
Commands, Representations & Settings
  1. PyMOL Commands
  2. Settings (Documented)
    1. All


050429science.pdf.jpg
  1. Representations
    1. Lines
    2. Sticks
    3. Ball and Sticks
    4. Cartoon
    5. Surface
    6. Mesh
    7. Spheres
    8. Dots
  2. Coloring
    1. Color
Physico-chemical Modeling
  1. Biochemical Properties
    1. Displaying biochemical properties
    2. Surfaces and Voids


Ribbon hh1.png
  1. Modeling and editing structures
    1. Editing Atoms
    2. Molecular sculpting
    3. Homology modeling
Images & Movies
  1. Image Manipulation
    1. Labels
    2. Photoshop/GIMP
    3. Stereo Figures
    4. Publication-quality images
    5. PovRay
  1. Making Movies
    1. Codecs


070816nature.pdf.jpg
Extending, Embedding & Scripting
  1. Scripting
    1. Example Scripts
    2. Script Library
  2. Plugins
    1. Electrostatics and energy minimization.
      1. APBS Plugin
      2. Protein_contact_potential
    2. rtools
    3. Tutorial on writing plugins
    4. Others
  1. High-Level Applications
    1. Crystallography Applications
      1. Symmetry|Symmetry
      2. Electron Density
    2. NMR Applications
      1. Working with Structure Families
    3. Superimposition and RMSD
      1. NMR Restraints and Analysis
Third Party Applications
  1. O
  2. SURFNET


080602cnen.pdf.jpg
  1. Python Integration
  2. PyMol_Integration
    1. Nuccyl -- Nuccyl is a great PyMol extension
    2. CASTp -- Binding and Active site prediction
    3. CCTBX -- Computational Crystallography Toolbox
    4. ProMOL
    5. S2S
    6. Arbitrary_Graphics_Objects
Retrieved from "http://pymolwiki.org/index.php?title=Talk:TOPTOC&oldid=5419"