RPR-SX-PDB

Analyzing PDB files

 

Keywords:  Practical work with the PDB, the R bio3d package

 

 

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Abstract

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This unit ...

Prerequisites

You need to complete the following units before beginning this one:

• BIN-PDB

 

Objectives

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Outcomes

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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: Integrated Unit

This unit should be submitted for evaluation for a maximum of 10 marks. Details TBD.

 

Contents

Compute with structures

 

To practice actual computations with structures we'll use the Grant lab's bio3d package in R.

Task:

• Open an RStudio session, and load the BCH441 project.
• Bring code and data resources up to date:
  • pull the most recent version of the project from GitHub
  • type init() to load the most recent files and functions.
• Study and work through the code in the BCH441_A05.R script.
• There are a number of questions in the code, it would be good if you don't gloss over them but try to answer them for yourself. Especially the questions about the final histogram: without interpretation, without learning something interesting about biology from the plot, all this is just Cargo Cult.

 

 

Further reading, links and resources

 

Notes

 

Self-evaluation

 

 

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If in doubt, ask! If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.

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About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2017-08-05

Version:

0.1

Version history:

• 0.1 First stub

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