Difference between revisions of "BIN-SX-Superposition"
Jump to navigation
Jump to search
Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.
m |
m |
||
| (4 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
<div id="ABC"> | <div id="ABC"> | ||
| − | <div style="padding:5px; border:1px solid #000000; background-color:# | + | <div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;"> |
Structure Superposition | Structure Superposition | ||
| − | <div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:# | + | <div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; "> |
(Structure superposition and superposition-derived alignment) | (Structure superposition and superposition-derived alignment) | ||
</div> | </div> | ||
| Line 10: | Line 10: | ||
| − | <div style="padding:5px; border:1px solid #000000; background-color:# | + | <div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;"> |
<div style="font-size:118%;"> | <div style="font-size:118%;"> | ||
<b>Abstract:</b><br /> | <b>Abstract:</b><br /> | ||
| Line 61: | Line 61: | ||
| − | |||
{{Smallvspace}} | {{Smallvspace}} | ||
| Line 77: | Line 76: | ||
{{Task|1= | {{Task|1= | ||
| − | * Read the introductory notes on {{ABC-PDF|BIN-SX-Superposition|the optimal superposition of protein 3D structures | + | * Read the introductory notes on {{ABC-PDF|BIN-SX-Superposition|the optimal superposition of protein 3D structures}} |
| − | * Browse over the [http://en.wikipedia.org/wiki/Structural_alignment Wikipedia article on '''Structural Superposition'''] <small>(although the article is called "Structural Alignment")</small>. | + | * Browse over the [http://en.wikipedia.org/wiki/Structural_alignment Wikipedia article on '''Structural Superposition'''] <small>(although the article is called "Structural Alignment")</small>. |
}} | }} | ||
| − | + | Put this into practice with ChimeraX: | |
| − | |||
| − | |||
| + | {{ABC-unit|RPR-ChimeraX_remote.R}} | ||
{{Vspace}} | {{Vspace}} | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
{{Vspace}} | {{Vspace}} | ||
| Line 123: | Line 98: | ||
:2017-08-05 | :2017-08-05 | ||
<b>Modified:</b><br /> | <b>Modified:</b><br /> | ||
| − | : | + | :2020-09-26 |
<b>Version:</b><br /> | <b>Version:</b><br /> | ||
| − | : | + | :2.0 |
<b>Version history:</b><br /> | <b>Version history:</b><br /> | ||
| + | *2.0 Move core of the Chimera practice into a Chimera remote-control script | ||
*1.0 First live version | *1.0 First live version | ||
*0.1 First stub | *0.1 First stub | ||
| Line 135: | Line 111: | ||
[[Category:ABC-units]] | [[Category:ABC-units]] | ||
{{UNIT}} | {{UNIT}} | ||
| − | {{ | + | {{LIVE}} |
</div> | </div> | ||
<!-- [END] --> | <!-- [END] --> | ||
Latest revision as of 06:57, 28 September 2020
Structure Superposition
(Structure superposition and superposition-derived alignment)
Abstract:
This unit discusses the concepts and practice of structural superposition.
|
Objectives:
|
Outcomes:
|
Deliverables:
Prerequisites:
This unit builds on material covered in the following prerequisite units:
Contents
Evaluation
Evaluation: NA
This unit is not evaluated for course marks.
Contents
Task:
- Read the introductory notes on the optimal superposition of protein 3D structures
- Browse over the Wikipedia article on Structural Superposition (although the article is called "Structural Alignment").
Put this into practice with ChimeraX:
Task:
- Open RStudio and load the
ABC-unitsR project. If you have loaded it before, choose File → Recent projects → ABC-Units. If you have not loaded it before, follow the instructions in the RPR-Introduction unit. - Choose Tools → Version Control → Pull Branches to fetch the most recent version of the project from its GitHub repository with all changes and bug fixes included.
- Type
init()if requested. - Open the file
RPR-ChimeraX_remote.Rand follow the instructions.
Note: take care that you understand all of the code in the script. Evaluation in this course is cumulative and you may be asked to explain any part of code.
About ...
Author:
- Boris Steipe <boris.steipe@utoronto.ca>
Created:
- 2017-08-05
Modified:
- 2020-09-26
Version:
- 2.0
Version history:
- 2.0 Move core of the Chimera practice into a Chimera remote-control script
- 1.0 First live version
- 0.1 First stub
This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.
