php require_once("fileinfo.php"); require_once( "relativePath.php"); $basedir = dirname($_SERVER["SCRIPT_NAME"]); ?> BCH622 : Structure of Biological Macromolecules

This is the home page for the Spring course - Structure of Biological Macromolecules - taught by Dave and Jane Richardson. Major revisions 2014 & 2021, some revisions each year.
We will discuss in class where and how to get further information

Meanwhile, if you are just poking into what the class might be like: We will follow the scheme of previous years with the first half class lectures, discussion, and assigned homework worksheets. The second half will be individual student projects mostly worked on as home work, but explained and discussed as interactively as we can manage with the whole group.
As a note: The cryoEM revolution is alive and active at Duke, and we will see how that gives a new way to determine macromolecular structures, and see how atomic models from cryoEM have somewhat different properties than models from x-ray crystallography - each with different issues of reliability and validation.

The table below will become a source of class materials - handouts, worksheets, and kinemage files. Two "flavors" of hyperlinks can be found in these two columns. The Subject column will contain links to other pages for display (or printing). The downloads column will contain links to files - typically kinemages - which you should download for use on your computer.

Depending on your browser's setup, certain files may be displayed rather than downloaded. In this case, you'll need to force the download by either "right-clicking" or control-clicking the link.



Subject ../downloads
click to download  ( )=optional
2021: Jan 22: assignment for Jan 29 ----
1) Macromolecular Structure &
Interactive Computer Graphics
1-General Information
1-Using KiNG
Intro Lesson: Getting Comfortable with Protein Geometry
HTML ||  download arrow 622introWrksht.pdf (~60KB) download arrow 622introWrksht.doc (~200KB)
files for intro graphics assignment:

ANATAX WEB VERSION -- View the on-line HTML version (or download PDFs) of the annotated Anatomy and Taxonomy of Protein Structure ("AnaTax"). For background on this week's lesson, read chapter 1 in AnaTax, and also chapter 1 in the Liljas text. If you don't yet have your own access to the textbook, the free read "inside" on Amazon includes the first 3 chapters.

2- H-BONDS LESSON + HELIX LESSON

2021: Jan 29: assignment for Feb 5

2) H-bonds Lesson and HELIX Lesson
Kinemage for this lesson:
  • download arrow 2hmqHelixExtras.kin (20KB)
  • download arrow general-noGPIVpreP_whbkg.kin.gz (9MB)
  • download arrow 2tma.kin (52KB)
  • download arrow 2mlt.a.kin (20KB)
  • download arrow 2cyp.kin (164KB)
  • If interactive KiNG fails in AnaTax:
    2021: Feb 5: assignment for Feb 12 ---
    3) All-atom Contact Analysis:
    Files for this lesson:
    2021: Feb 12: assignment for Feb 19
    5) Beta Proteins: (α/β)8 & Greek Key

    Kinemages for this lesson:
    2021: Feb 19: assignment for Feb 26
    4) Structural Roles of Amino Acids and Mutations
    Files for this lesson:


    MACROMOLECULAR CRYSTALLOGRAPHY
  • download arrow   (15MB) 12 lectures worth of notes: MacroMolecularCrystallography2009.pdf

  • 2020: Feb 13: assignment for Feb 20

    5) Resolution and Validation

    (Ref. online notes:elasticScattering
    /teaching/BCH681/2013BCH681/
    elasticScattering)
  • download arrow 622notes_EDMaps-resolution.pdf (893KB)

  • download arrow myoglobin2NRLwith1.5Awave.pdf

  • download arrow  622-wrksht-resolution-validation.pdf

  • Files for this lesson:
  • download arrow 1.0_1HJ8_1.0A.kin (340KB)
  • download arrow 1.0_1hj8.omap.gz (2.7MB)
  • download arrow 2.8_1C9P_2.8A.kin (165KB)
  • download arrow 2.8_1c9p.omap.gz (254KB)
  • download arrow 1JIRon1S83_Arg66_supr.kin (1.5MB)
  • Reference papers:
  • download arrow 2018Richardson_CCP4val_ActaD74.pdf (3.3MB)
  • MolProbity: download arrow 2018Williams_MolProbity_ProtSci27.pdf(4.6MB)
  • 2020: Feb 20: assignment for Feb 27
    CryoEM
  • assignment:   CryoEM Lesson
    download arrow WrkSht5-cryoEM_2018.doc (970KB)
  • Files for this lesson:
  • download arrow 5a1a_beta-gal_barrel_ribbons.kin (1.8MB)
  • download arrow 5a1a_beta-galactosidase_2.2A.kin (5.5MB)
  • download arrow 5gan_spliceosome_tri-snRNP.kin (16.3MB)
  • Reference papers:
  • download arrow 2018Richardson_CCP4val_ActaD74.pdf (3.3MB)
  • Reference papers:
  • download arrow 2019CryoEM-BB47CH08_Nagai_001-025].pdf (3.3MB)
  • download arrow 2019CryoEM-CRusso_hi-res_strategies.pdf (3.3MB)

  • 2020: Feb 27: assignment for Mar 5
    Computer Graphics: Making kinemages using KiNG

    KiNG has an internal manual available as one of its menu items; the same information is available in the download arrow king-manual.pdf(240KB). The pdf-format manual is included in the KiNG download with two other pdf documents: The Kinemage File Format (download arrow format-kinemage.pdf, 140KB) and Hacking KiNG (download arrow hacking-king.pdf, 160KB) a guide to KiNG's code and libraries. Instructions for using KiNG are available as a basics guide in html form or as a PDF (download arrow QuickStartKiNG.pdf(35KB)). The other documents linked above also contain usage instructions.


    Files for this exercise:

    BCH622 class projects:

         An oral presentation report, mainly using interactive 3D graphics (kinemage or other), about some topic in 3D macromolecular structure that interests you and connects with the course materials: protein, RNA, DNA, or their complexes with each other or carbohydrates or small-molecule ligands. The topic question can be structure/function relationships within a specific biological system or a more general question or comparison across multiple structures at the atomic level in 3D.
         A minor component is either to construct a publication-suitable 2D image that clearly conveys one of your important points or else to work on improving the most relevant Wikipedia article.
         You will give a couple of progress reports in class, and do your final presentation at the end of the semester.


    2020: Mar 12 Spring Break
    2020: Mar 19 in-class presentation of initial project ideas     For the first class after spring break, each person will explain their project idea, showing a simple kinemage from one relevant PDB file, one relevant literature reference, and one reasonably relevant Wikipedia reference.
    Hand in on paper a short paragraph describing your project idea.



    Possible: In-class model-to-map fitting the "real way"

    No general assignment, suggest review
    622-wrksht-resolution-validation.
    Homework == Work on Project

    optional consultation about problems with project details
    2020: Through April in class:
    ... in-progress reports


    No general assignment

    Homework == Work on Project

    2020 sometime in class: EditingWikipedia_forScientists




    Homework == Edit Wikipedia article

    download arrow EditingWikipedia_forScientists_WP-BP_2015.doc (154KB)

    Homework == Work on Project


    Homework == Work on Project

    2020: Apr 30 "IN CLASS" (EXAM WEEK)
    PROJECT REPORTS




    Might need to adjust time/day...