This is the home page for the Spring course - Structure of Biological Macromolecules - taught by Dave and Jane Richardson. Revised 2014, Material specific for Spring 2015 added in, and modified again for 2016. So no surprise that the course is being revised for 2018.
Wednesday Jan 10 622 WEBSITE IS NOTED NOT CURRENT! (Hopefully this will gradually change, week by week)
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, hands-on model building, discussion, assigned homework worksheets, etc. 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 tease: The cryoEM revolution is alive and active at Duke, and we will see how that gives a new way to not only see macromolecules, but understand how atomic models from cryoEM have different properties than models from x-ray crystallography - 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
2016: Jan 14: assignment for Jan 21
1) Macromolecular Structure &
Interactive Computer Graphics (rev.20150109)
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:
View the on-line HTML version (or download PDFs) of the annotated Anatomy and Taxonomy of Protein Structure. "AnaTax"
2016: Jan 21: assignment for Jan 28
2) H-bonds Lesson and HELIX Lesson
Kinemage for this lesson:
2016: Jan 28: assignment for Feb 4 ---
3) All-atom Contact Analysis:
Files for this lesson:
2016: Feb 4: assignment for Feb 11
4) Structural Roles of Amino Acids and Mutations
Files for this lesson:
  • download arrow c1Basics-A-KiNG.kin (123KB)
  • download arrow 1994_Hemmingsen_TyrCorner_ProSci-cvr.pdf (3.1MB)
  • download arrow 1gcr_Tyr_corners_2015.kin (1.6MB)
  • download arrow 1gcrFH.pdb (263KB)
  • download arrow LRI_ColoringBook.pdf (1.3MB)
  • 2016: Feb 11: assignment for Feb 18
    5) Motions and Hemoglobin
    class notes and handouts
    Files for this lesson:
  • download arrow c6FldFlx-KiNG_mod.kin (123KB)
  • download arrow HbAllo-KiNGques.kin (123KB)
  • download arrow c8HthTF.kin (317KB)
  • download arrow c15Immun.kin (375KB)
  • Hemoglobin tetramer ribbon (Big file!):
  • download arrow 2dn1-2_ribbon_Oxy-Deoxy_KiNG.kin (15.4MB) (in class)
  • original pair of papers:
    download arrow Perutz-1970.pdf (1.3MB)

  • 2016: Feb 18: assignment for Feb 25

    6) Resolution and Validation
    in-class notes: diffraction & resolution
  • download arrow 622-20160114-in-class.pdf (19KB)
  • download arrow myoglobin2NRLwith1.5Awave.pdf (212KB)
  • download arrow 622notes_EDMaps-resolution.pdf (893KB)
  • WorkSheets:
  • download arrow Wksht_resolution_bch622.pdf (46KB)
  • download arrow Wrksht_validation-20160218.pdf (81KB)

  • 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 2013-Richardson_validation Review_COSB23.pdf (1.9MB)
  • MolProbity: download arrow 2010-ChenActaCrystD66.pdf (1.6MB)
  • View the on-line HTML version (or download PDFs) of the annotated Anatomy and Taxonomy of Protein Structure. "AnaTax"

    2016: Feb 25: assignment for Mar 3
    7) Beta Proteins: (α/β)8 & Greek Key
    Kinemages for this lesson: files for this lesson:
    2016: Mar 3 in-class:
    8)... β structure continuing
       Greek key topology, esp. jellyroll around    flavored pair of antiparallel β
       roll the β barrel offset pairs of parallel β
    Mar 3: assignment for Mar 10
    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.

    2016 Mar 10 in-class: Discussion of project development and presentation strategy
          Mar 10 assignment for Mar 24 (see anticipated in-class goals for Mar 24)
    2016: Mar 17 Spring Break
    2016: Mar 24 in-class presentation of initial project ideas     For the first class after spring break (Mar 24), 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.



    2015: Mar 26 In-class model-to-map fitting the "real way"

    No general assignment, suggest review
    Homework == Work on Project

    optional consultation about problems with project details
    2015: Apr 2 in class:
    Group 1 in-progress reports

    No general assignment

    Homework == Work on Project

    2015: Apr 9 in class:
    Group 2 in-progress reports

    No general assignment

    Homework == Work on Project

    download arrow EditingWikipedia_forScientists_WP-BP_2015.doc (154KB)
    2015: Apr 16 in class:
    Group 1 in-progress reports

    No general assignment

    Homework == Work on Project

    2015: Apr 23 in class:
    Group 2 in-progress reports

    No general assignment

    Homework == Work on Project

    2015: Apr 30 "IN CLASS" (EXAM WEEK)

    Might need to adjust time/day...