Difference between revisions of "RPR-SX-PDB"
Jump to navigation
Jump to search
m (Boris moved page BIN-SX-PDB to RPR-SX-PDB without leaving a redirect) |
m |
||
| Line 27: | Line 27: | ||
<div id="ABC-unit-framework"> | <div id="ABC-unit-framework"> | ||
== Abstract == | == Abstract == | ||
| − | <!-- included from "../components/ | + | <!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "abstract" --> |
... | ... | ||
| Line 35: | Line 35: | ||
== This unit ... == | == This unit ... == | ||
=== Prerequisites === | === Prerequisites === | ||
| − | <!-- included from "../components/ | + | <!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "prerequisites" --> |
<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" --> | <!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" --> | ||
You need to complete the following units before beginning this one: | You need to complete the following units before beginning this one: | ||
*[[BIN-PDB]] | *[[BIN-PDB]] | ||
| − | |||
{{Vspace}} | {{Vspace}} | ||
| Line 45: | Line 44: | ||
=== Objectives === | === Objectives === | ||
| − | <!-- included from "../components/ | + | <!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "objectives" --> |
... | ... | ||
| Line 52: | Line 51: | ||
=== Outcomes === | === Outcomes === | ||
| − | <!-- included from "../components/ | + | <!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "outcomes" --> |
... | ... | ||
| Line 59: | Line 58: | ||
=== Deliverables === | === Deliverables === | ||
| − | <!-- included from "../components/ | + | <!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "deliverables" --> |
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" --> | <!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" --> | ||
*<b>Time management</b>: 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. | *<b>Time management</b>: 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. | ||
| Line 71: | Line 70: | ||
=== Evaluation === | === Evaluation === | ||
| − | <!-- included from "../components/ | + | <!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "evaluation" --> |
<!-- included from "ABC-unit_components.wtxt", section: "eval-none" --> | <!-- included from "ABC-unit_components.wtxt", section: "eval-none" --> | ||
<b>Evaluation: NA</b><br /> | <b>Evaluation: NA</b><br /> | ||
| Line 82: | Line 81: | ||
<div id="BIO"> | <div id="BIO"> | ||
== Contents == | == Contents == | ||
| − | <!-- included from "../components/ | + | <!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "contents" --> |
| − | ... | + | |
| + | |||
| + | == Compute with structures == | ||
| + | |||
| + | {{Vspace}} | ||
| + | |||
| + | To practice actual computations with structures we'll use the Grant lab's bio3d package in '''R'''. | ||
| + | |||
| + | {{task|1 = | ||
| + | |||
| + | * 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 <code>init()</code> to load the most recent files and functions. | ||
| + | * Study and work through the code in the <code>BCH441_A05.R</code> 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. | ||
| + | |||
| + | }} | ||
| + | |||
| + | {{Vspace}} | ||
| + | |||
| + | |||
| + | |||
{{Vspace}} | {{Vspace}} | ||
| Line 97: | Line 118: | ||
== Notes == | == Notes == | ||
| − | <!-- included from "../components/ | + | <!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "notes" --> |
<!-- included from "ABC-unit_components.wtxt", section: "notes" --> | <!-- included from "ABC-unit_components.wtxt", section: "notes" --> | ||
<references /> | <references /> | ||
| Line 107: | Line 128: | ||
<div id="ABC-unit-framework"> | <div id="ABC-unit-framework"> | ||
== Self-evaluation == | == Self-evaluation == | ||
| − | <!-- included from "../components/ | + | <!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "self-evaluation" --> |
<!-- | <!-- | ||
=== Question 1=== | === Question 1=== | ||
Revision as of 04:38, 31 August 2017
Analyzing PDB files
Keywords: Practical work with the PDB, the R bio3d package
Contents
Sorry!
This page is only a stub; it is here as a placeholder to establish the logical framework of the site but there is no significant content as yet. Do not work with this material until it is updated to "live" status.
Abstract
...
This unit ...
Prerequisites
You need to complete the following units before beginning this one:
Objectives
...
Outcomes
...
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.
- Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.
Evaluation
Evaluation: NA
- This unit is not evaluated for course marks.
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.Rscript. - 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
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.
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
This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.
