Expected Preparations:

  [BIN-ALI]
Alignment 		  [BIN-SX]
Chimera 		  [RPR-SX]
PDB 		 
  The units listed above are part of this course and contain important preparatory material.  
Keywords: Structure superposition and superposition-derived alignment
Objectives:

This unit will …

  • … introduce the concepts of structural superposition;

  • … demonstrate the outcomes of superpositions in the presence and absence of sigificant sequence similarity;

  • … point you to servers that allow superposition-based searches for similar proteins

  • … list tutorials for superposition with Chimera and bio3d.

 Outcomes:

After working through this unit you …

  • … can discover proteins that are structurally similar to a query;

  • … can compute a structural superposition with Chimera or bio3d;

  • … derive a superposition-based alignment.

Deliverables:

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.

Evaluation:

NA: This unit is not evaluated for course marks.

Contents

This unit discusses the concepts and practice of structural superposition.

Task…

Put this into practice with ChimeraX:

Task…

  • Open RStudio and load the ABC-units R 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. This ensures that your data and code remain up to date when we update, or fix bugs.
  • Type init() if requested.
  • Open the file RPR-ChimeraX_remote.R and 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.

 

Questions, comments

If in doubt, ask! If anything about this contents is not clear to you, do not proceed but ask for clarification. If you have ideas about how to make this material better, let’s hear them. We are aiming to compile a list of FAQs for all learning units, and your contributions will count towards your participation marks.

Improve this page! If you have questions or comments, please post them on the Quercus Discussion board with a subject line that includes the name of the unit.

References

Page ID: BIN-SX-Superposition

Author:
Boris Steipe ( <boris.steipe@utoronto.ca> )
Created:
2017-08-05
Last modified:
2022-09-14
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
Tagged with:
–  Unit
–  Live
–  Has lecture slides
–  Links to R course project

 

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