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 revision 2014, some revisions each year and material specific for each year added in.
WE WILL DISCUSS WHAT AND WHERE TO GET INFORMATION IN CLASS
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.
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../downloads
click to download ( )=optional |
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2022: Jan 7: assignment for Jan 14 ---- 1) Macromolecular Structure & Interactive Computer Graphics 1-General Information 1-Using KiNG Intro Lesson: Getting Comfortable with Protein Geometry  622introWrksht.pdf (~100KB)
622introWrksht.docx (~40KB)
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files for intro graphics assignment:
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ANATAX WEB VERSION View the on-line HTML version (or download PDFs) of the annotated Anatomy and Taxonomy of Protein Structure. "AnaTax" |
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2- H-BONDS LESSON + HELIX LESSON 2022: Jan 14: 622hbondWrksht-KiNG.pdf AND HbondPractice-KiNG.kin ARE GOODAS OF JAN 21: HELIX LESSON AND ITS KINEMAGES REPAIRED 2) H-bonds Lesson and HELIX Lesson
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Kinemage for this lesson:
2hmqHelixExtras.kin (20KB) general-noGPIVpreP_whbkg.kin.gz (9MB) 2tma.kin (52KB) 2mlt.a.kin (20KB) 2cyp.kin (164KB)
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2020: Jan 23: assignment for Jan 30 --- 3) All-atom Contact Analysis:
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Files for this lesson:
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2020: Jan 30: assignment for Feb 6 5) Beta Proteins: (α/β)8 & Greek Key
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Kinemages for this lesson:
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2020: Feb 6: assignment for Feb 13 4) Structural Roles of Amino Acids and Mutations
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Files for this lesson:
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MACROMOLECULAR CRYSTALLOGRAPHY
(15MB) 12 lectures worth of notes: MacroMolecularCrystallography2009.pdf
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2020: Feb 13: assignment for Feb 20 5) Resolution and Validation (Ref. online notes:elasticScattering /teaching/BCH681/2013BCH681/ elasticScattering) 622notes_EDMaps-resolution.pdf (893KB)
myoglobin2NRLwith1.5Awave.pdf
622-wrksht-resolution-validation.pdf |
Files for this lesson: 1.0_1HJ8_1.0A.kin (340KB) 1.0_1hj8.omap.gz (2.7MB) 2.8_1C9P_2.8A.kin (165KB) 2.8_1c9p.omap.gz (254KB) 1JIRon1S83_Arg66_supr.kin (1.5MB) 2018Richardson_CCP4val_ActaD74.pdf (3.3MB)
2018Williams_MolProbity_ProtSci27.pdf(4.6MB)
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| 2020: Feb 20: assignment for Feb 27 |
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| CryoEM | ||
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WrkSht5-cryoEM_2018.doc (970KB) |
Files for this lesson:
5a1a_beta-gal_barrel_ribbons.kin (1.8MB)
5a1a_beta-galactosidase_2.2A.kin (5.5MB)
5gan_spliceosome_tri-snRNP.kin (16.3MB)
2018Richardson_CCP4val_ActaD74.pdf (3.3MB)
2019CryoEM-BB47CH08_Nagai_001-025].pdf (3.3MB)
2019CryoEM-CRusso_hi-res_strategies.pdf (3.3MB)
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| 2020: Feb 27: assignment for Mar 5 | ||
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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 |
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622makeKinTut2016.pdf (85KB) REVISED 2016 |
Files for this exercise:
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BCH622 class projects: |
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| 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. | ||
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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 | |
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2020: Through April in class: ... in-progress reports No general assignment |
Homework == Work on Project | |
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2020 sometime in class: EditingWikipedia_forScientists |
Homework == Edit Wikipedia article EditingWikipedia_forScientists_WP-BP_2015.doc (154KB)
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Homework == Work on Project | |
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Homework == Work on Project | |
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2020: Apr 30 "IN CLASS" (EXAM WEEK) PROJECT REPORTS |
Might need to adjust time/day... | |
AminoAcidsColor.jpg