Difference between revisions of "RPR-SX-PDB"

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<div style="padding:5px; border:4px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
 
Analyzing PDB files
 
Analyzing PDB files
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  </div>
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<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
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(Practical work with the PDB, the R bio3d package)
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  {{Vspace}}
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</div>
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<div class="keywords">
 
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<b>Keywords:</b>&nbsp;
 
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Practical work with the PDB, the R bio3d package
 
 
</div>
 
</div>
  
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{{Vspace}}
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{{Smallvspace}}
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__TOC__
 
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{{Vspace}}
 
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{{LIVE}}
 
  
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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
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<div style="font-size:118%;">
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<b>Abstract:</b><br />
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</div>
 
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<div id="ABC-unit-framework">
 
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== Abstract ==
 
 
<section begin=abstract />
 
<section begin=abstract />
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<!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "abstract" -->
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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 <tt>bio3D::</tt>.
−
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.
 
 
<section end=abstract />
 
<section end=abstract />
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</div>
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{{Vspace}}
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<!-- ============================ -->
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<hr>
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<table>
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== This unit ... ==
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<tr>
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=== Prerequisites ===
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<td style="padding:10px;">
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<!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "prerequisites" -->
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<b>Objectives:</b><br />
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<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" -->
 
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You need to complete the following units before beginning this one:
 
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*[[BIN-PDB|BIN-PDB (The RCSB-PDB Structure Database)]]
 
−
 
 
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{{Vspace}}
 
−
 
 
−
 
 
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=== Objectives ===
 
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<!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "objectives" -->
 
 
This unit will ...
 
This unit will ...
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* ... introduce the bio3d package;
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* ... introduce the <tt>bio3D::</tt> package;
 
* ... demonstrate quantitative analysis of PDB files;
 
* ... demonstrate quantitative analysis of PDB files;
 
* ... teach plotting techniques for density plots;
 
* ... teach plotting techniques for density plots;
 
* ... explore database-scale work with PDB files.
 
* ... explore database-scale work with PDB files.
 +
</td>
 +
<td style="padding:10px;">
 +
<b>Outcomes:</b><br />
 +
After working through this unit you ...
 +
* ... are familar with PDB objects in the <tt>bio3D::</tt> package;
 +
* ... can investigate features of PDB structures both in individual structures and collections of structures, and plot and interpret the results.
 +
</td>
 +
</tr>
 +
</table>
 +
<!-- ============================  -->
 +
<hr>
 +
<b>Deliverables:</b><br />
 +
<section begin=deliverables />
 +
<li><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.</li>
 +
<li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li>
 +
<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
 +
<section end=deliverables />
 +
<!-- ============================  -->
 +
<hr>
 +
<section begin=prerequisites />
 +
<b>Prerequisites:</b><br />
 +
This unit builds on material covered in the following prerequisite units:<br />
 +
*[[BIN-PDB|BIN-PDB (The RCSB-PDB Structure Database)]]
 +
<section end=prerequisites />
 +
<!-- ============================  -->
 +
</div>
  
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{{Vspace}}
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{{Smallvspace}}
  
  
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=== Outcomes ===
 
−
<!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "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.
 
  
−
{{Vspace}}
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{{Smallvspace}}
  
  
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=== Deliverables ===
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__TOC__
−
<!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "deliverables" -->
 
−
<!-- 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.
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-journal" -->
 
−
*<b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-insights" -->
 
−
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 
  
 
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=== Evaluation ===
 
=== Evaluation ===
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<!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "evaluation" -->
 
  
  
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This learning unit can be evaluated for a maximum of 6 marks. If you want to submit tasks for this unit for credit you have the following options. If you have any questions about these options, discuss on the mailing list.
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This learning unit can be evaluated for a maximum of 5 marks ...
 +
<ol>
 +
<li>Create a new page on the student Wiki as a subpage of your User Page.</li>
 +
<li>Put all of your writing to submit on this one page.</li>
 +
<li>When you are done with everything, go to the [https://q.utoronto.ca/courses/180416/assignments Quercus '''Assignments''' page] and open the first Learning Unit that you have not submitted yet. Paste the URL of your Wiki page into the form, and click on '''Submit Assignment'''.</li>
 +
</ol>
 +
 
 +
Your link can be submitted only once and not edited. But you may change your Wiki page at any time. However only the last version before the due date will be marked. All later edits will be silently ignored.
 +
 
 +
{{Smallvspace}}
  
 
; Short Report option
 
; Short Report option
 
:'''1.''' Create a new page on the student Wiki as a subpage of your User Page.
 
:'''1.''' Create a new page on the student Wiki as a subpage of your User Page.
 
:'''2.''' Select a unique set of fifteen representative PDB structures by issuing the command:
 
:'''2.''' Select a unique set of fifteen representative PDB structures by issuing the command:
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<source lang="R">
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<pre>
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(myPDBs <- selectPDBrep(15))
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( myPDBs <- selectPDBrep(n = 15, forCredit = TRUE) )
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</source>
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</pre>
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:'''3.''' Analyze the distribution of H-bonds in helices and strands of your fifteen structures. Interpret your findings: what is the source of the difference, what seems to be the lowest energy distance between N...O in a Hydrogen bond?
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:'''3.''' Analyze the distribution of H-bonds in helices and strands of your fifteen structures. Interpret your findings: what is the source of the difference, '''what''' seems to be the lowest energy distance between N...O in a Hydrogen bond, '''how''' does this appear in our data and '''why''' is this so? <small>(Think! This question is a bit subtle, but can be answered by just thinking about it.)</small>
−
:'''4.''' Count the number of cis-peptide bonds in your structures. Do this separately for prolines, and for all other residues. Do you find that X-Pro cis-peptide bonds are more frequent than others? Why is that?
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:'''4.''' Count the number of ''cis''-peptide bonds in your structures. Do this separately for prolines, and for all other residues. Do you find that X-Pro ''cis''-peptide bonds are more frequent than others? Why is that? <small>(Think! Are you identifying the correct bonds? How do you know? How did you test?)</small>
−
:'''5.''' Plot chi1 torsion angles of amino acid sidechains againt chi2 torsion angles to analyze sidechain rotamer distributions. Aim for a publication quality plot and include the plot and its caption in your report. Choose one of the following amino acids for your analysis:
+
:'''5.''' Plot chi1 torsion angles of amino acid sidechains againt chi2 torsion angles to analyze sidechain rotamer distributions. Aim for a publication quality plot and include the plot and its caption in your report. Randomly choose '''one''' amino acid for analysis by issuing the following command:
−
tyrosine, phenylalanine, histidine, tryptophan, isoleucine, leucine, asparagine or aspartic acid. Interpret the results.
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<pre>
−
:'''6.''' Form matters. Be neat, and concise! Be sure to include a list of your PDB IDs in your report! Make sure your process is documented, your results are presented, and that everything is interpreted. At the end of your report, include a section that contains all of the R script(s) you have written for your analysis. Make sure that your scripts are clean, error-free and commented. Also make absolutely sure that you have referenced all contributions that are not originally your own.
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selectChi2()
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:'''7.''' When you are done with your report, add the following category tag to the page:
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</pre>
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::<code><nowiki>[[Category:Eval-RPR-SX-PDB]]</nowiki></code>
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:... and paste the entire line of the output into your submission.
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:'''Do not''' change your submission page after this tag has been added. The page will be marked and the category tag will be removed by the instructor.
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: When you have produced your plot, interpret the results.
−
 
+
:'''6.''' Form matters. Be neat, and concise! Be sure to include the list of the PDB IDs you selected in your report! Make sure your process is documented, your results are presented, and that everything is interpreted. At the end of your report, include a section that contains all of the R script(s) you have written for your analysis. Make sure that your scripts are clean, error-free and commented. Also make absolutely sure that you have referenced all contributions that are not originally your own.
 +
:'''7.''' When you are done with everything, submit the page via Quercus as described above.
 
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<div id="BIO">
 
 
== Contents ==
 
== Contents ==
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<!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "contents" -->
 
  
  
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== Further reading, links and resources ==
 
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<!-- {{#pmid: 19957275}} -->
 
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<!-- {{WWW|WWW_GMOD}} -->
 
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<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
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== Notes ==
 
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<!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "notes" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "notes" -->
 
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<references />
 
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{{Vspace}}
 
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</div>
 
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<div id="ABC-unit-framework">
 
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== Self-evaluation ==
 
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<!-- included from "../components/RPR-SX-PDB.components.wtxt", section: "self-evaluation" -->
 
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<!--
 
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=== Question 1===
 
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Question ...
 
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<div class="toccolours mw-collapsible mw-collapsed" style="width:800px">
 
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Answer ...
 
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Answer ...
 
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----
 
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<b>If in doubt, ask!</b> 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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<div class="about">
 
<div class="about">
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:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
<b>Modified:</b><br />
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:2017-10-17
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:2020-09-22
 
<b>Version:</b><br />
 
<b>Version:</b><br />
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:1.0
+
:1.2
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
 +
*1.2 Edit policy update
 +
*1.1 Maintenance
 
*1.0 First live version
 
*1.0 First live version
 
*0.1 First stub
 
*0.1 First stub
 
</div>
 
</div>
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[[Category:ABC-units]]
 
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<!-- included from "ABC-unit_components.wtxt", section: "ABC-unit_footer" -->
 
  
 
{{CC-BY}}
 
{{CC-BY}}
  
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[[Category:ABC-units]]
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{{EVAL}}
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{{LIVE}}
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{{EVAL}}
 
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Latest revision as of 20:24, 13 October 2020

Analyzing PDB files

(Practical work with the PDB, the R bio3d package)


 


Abstract:

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::.

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.

    • Prerequisites:
    This unit builds on material covered in the following prerequisite units:


     



     



     


    Evaluation

    This learning unit can be evaluated for a maximum of 5 marks ...

    1. Create a new page on the student Wiki as a subpage of your User Page.
    2. Put all of your writing to submit on this one page.
    3. When you are done with everything, go to the Quercus Assignments page and open the first Learning Unit that you have not submitted yet. Paste the URL of your Wiki page into the form, and click on Submit Assignment.

    Your link can be submitted only once and not edited. But you may change your Wiki page at any time. However only the last version before the due date will be marked. All later edits will be silently ignored.


     
    Short Report option
    1. Create a new page on the student Wiki as a subpage of your User Page.
    2. Select a unique set of fifteen representative PDB structures by issuing the command:
    ( myPDBs <- selectPDBrep(n = 15, forCredit = TRUE) )
    3. Analyze the distribution of H-bonds in helices and strands of your fifteen structures. Interpret your findings: what is the source of the difference, what seems to be the lowest energy distance between N...O in a Hydrogen bond, how does this appear in our data and why is this so? (Think! This question is a bit subtle, but can be answered by just thinking about it.)
    4. Count the number of cis-peptide bonds in your structures. Do this separately for prolines, and for all other residues. Do you find that X-Pro cis-peptide bonds are more frequent than others? Why is that? (Think! Are you identifying the correct bonds? How do you know? How did you test?)
    5. Plot chi1 torsion angles of amino acid sidechains againt chi2 torsion angles to analyze sidechain rotamer distributions. Aim for a publication quality plot and include the plot and its caption in your report. Randomly choose one amino acid for analysis by issuing the following command:
    selectChi2()
    ... and paste the entire line of the output into your submission.
    When you have produced your plot, interpret the results.
    6. Form matters. Be neat, and concise! Be sure to include the list of the PDB IDs you selected in your report! Make sure your process is documented, your results are presented, and that everything is interpreted. At the end of your report, include a section that contains all of the R script(s) you have written for your analysis. Make sure that your scripts are clean, error-free and commented. Also make absolutely sure that you have referenced all contributions that are not originally your own.
    7. When you are done with everything, submit the page via Quercus as described above.
     


    Contents

    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.
    • 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.


     


     



     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2020-09-22

    Version:

    1.2

    Version history:

    • 1.2 Edit policy update
    • 1.1 Maintenance
    • 1.0 First live version
    • 0.1 First stub

    CreativeCommonsBy.png This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.

    Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=RPR-SX-PDB&oldid=11874"