Expected Preparations:

  [BIN]
PDB 		 
  The units listed above are part of this course and contain important preparatory material.  
Keywords: Practical work with the PDB; the bio3d:: package
Objectives:

This unit will …

  • … introduce the bio3D:: package;

  • … demonstrate quantitative analysis of PDB files;

  • … teach plotting techniques for density plots;

  • … explore database-scale work with PDB files.

 Outcomes:

After working through this unit you …

  • … are familar with PDB objects in the bio3D:: package;

  • … can investigate features of PDB structures both in individual structures and collections of structures, and plot and interpret the results.

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:

Evaluation deliverables under revision:
While we are rebalancing formative feedback (advice) and summative feedback (grades) for this course, please ignore all instructions for the submission of assignments until this alert is removed.

 

Contents

PDB structures are complex objects to which we can apply a number of measures - but doing so requires that we can read and analyze them in the computer. In this unit we explore computational analysis of PDB structures using bio3D::.

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-SX-PDB.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: RPR-SX-PDB

Keywords: Practical work with the PDB; the bio3d:: package

Author:
Boris Steipe ( <boris.steipe@utoronto.ca> )
Created:
2017-08-05
Last modified:
2022-09-14
Version:
1.2
Version History:
–  1.2 Edit policy update
–  1.1 Maintenance
–  1.0 First live version
–  0.1 First stub
Tagged with:
–  Eval
–  Live
–  Evaluated unit
–  Has R code examples
–  Links to R course project

 

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