This is the home page for the Spring 2011 course - Structure of Biological Macromolecules - taught by Dave and Jane Richardson.

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
1) Macromolecular Structure & Interactive Computer Graphics General Information Using KiNG Intro Lesson: Getting Comfortable with Protein Geometry HTML ||   222introWrksht.pdf (72KB)	files for intro graphics assignment:  1a6m.kin.gz (464KB)  c6FldFlx.kin (796KB)  (c1Basics-A-KiNG.kin) (124KB)  (Demo5_4a.kin) (100KB)
2) H-bonds & Helices: Assignment: H-bonds & Helices H-bonds worksheet:  222hbondWrksht-KiNG.pdf (52KB) Helix worksheet:  HTML ||  222helixWrksht.pdf (148KB)	Kinemages for these two lessons:  HbondPractice-KiNG.kin (104KB)  2hmqHlx.kin (24KB)  general-noGPIVpreP_whbkg.kin.gz (9MB)  2tma.kin (52KB)  2mlt.a.kin (20KB)  2cyp.kin (164KB)  (c3Alpha.kin) (352KB)  (2erl_hlxContacts.kin) (76KB)
3) Beta Proteins: (α/β)8 & Greek Key assignment & worksheet:  HTML ||  222BetaWrksht_ab8_and_GkKey.pdf (62KB)	Kinemages for this lesson:  babarel8.kin (52KB)  ab8barrel.kin (60KB)  1tim_a.kin (96KB)  1E43_GkKey.kin (96KB)  StSurvey_kin4.kin (96KB) files for this lesson:  Lesk1989_ab8barrels.pdf (96KB)  Salemme_PropOfBSheets_short.pdf (96KB)
4) All-atom Contact Analysis: assignment & worksheet:  HTML ||  222contactAnalysisWrksht.pdf (68KB) tips on using Probe & Reduce:  HTML ||  222mageProbeUse.pdf (102KB)	Files for this lesson:  1999_Word_Condots_JMB.pdf (1.5MB)  Demo5_4b.kin (400KB)  1iftH.kin (340KB)  1IFTH.pdb (356KB)  3Dlit_tetr_CO_KiNG.kin  ubiquitin_1.31A_2012.pdb  ubiquitin_1.31A_2012-multi_map.kin
5) The Ribosome: assignment & worksheet:  HTML ||  222ribosomeWrksht.pdf (72KB)	Files for this lesson:  1ffk.bb.kin (696KB)  1ffk_5Sto38.kin (436KB)  1ffk5SHstack.kin (1.9MB)  1ffk5S_mcdots.kin (1.1MB)  1ffk_hlx7H.kin (433KB)  1s72_v_hlx7-con.kin (240KB)  1ffk_piece.pdb (38KB)  c7DNA.kin (160KB)  Ecoli70S_with_tRNAs.kin (2.4M)  Ecoli70S_ratchet_demo.kin (1.4M)  2000 Ban 50S Science paper (3.4MB)  2011 Dunkle 70S Science paper (1MB)
6) Crystallographic Model Building: assignment:  HTML ||  222mapfitWrksht.pdf (84KB) reading:   1999Branden-ch18.pdf reading:   1985MethEnz-edensity.pdf	Files for this lesson:  1mjfH.pdb (740KB)  1mjfHa.kin (380KB)  1mjf.omap.gz (1.5MB)  1BKRH.pdb (256KB)  1BKRH-contact.kin (496KB)  1bkr_later.kin (80KB)  1bkr_2FoFc.omap.gz (1.3MB)  cabenolH.pdb (240KB)  cabenolH.kin (244KB)  cabenol_2FoFc.omap.gz (404KB)  cabenol_FoFc.omap.gz (400KB)  301dH_mcCon.kin (156KB)  301d.omap.gz (116KB)
7) Resources for projects: Project suggestions for data-mining    222Project_suggestions_data-mining.pdf (84KB) Asn/Gln rotamer paper    1999Lovell_NQrot_PNAS.pdf (504KB) Editing kinemages with KiNG  HTML ||  222editWithKing.pdf (28KB) Kinemage construction tutorial    makeKinTut_inKiNG.pdf (86KB)	Files for this section:  VTF_noFlip100104_nDate_filtProt.txt.gz (file-level data) (1.2MB)  SS_nosym_232_T5200.kin.gz (3D disulfide kin) (1.1MB)  rota4400-SS_inChain.csv (multi-D disulfide spreadsheet) (264KB)  rota4400-Asn_all_psipsichi.kin.gz (3.2MB)  2AAIed.pdb (kin tutorial example file) (389KB)
Ramachandran-Plot Data Analysis: assignment & worksheet:  HTML ||  222RamaPlotDataWrksht.pdf (68KB) reading:   2003LovellProteins50.pdf	Files for this lesson:  rama4400-bch222-2011_short.csv.zip (5.1MB)  prepro-noGP_Blt30_wh.kin.gz (632KB)  rama4400_short_aaSort.kin.gz (4.6MB)  general-noGPIVpreP_justContours_atZ90.kin (96KB)
Sidechain Rotamer Data Analysis: assignment:  HTML ||  222rotamerPlotWrksht.pdf (84KB) reading:   2000LovellProteins40.pdf	Files for this lesson:  rota4400-gln_ptm.kin.gz (832KB)  1n83FH_Gln321_ecl_chi2.kin.gz (110KB)  rota4400-leu_byB.kin.gz (1.2MB)  1xwlFH-Leu473.kin.gz (184KB)  1xwlFH.pdb (820KB)  rota4400-Pro_cis-trans.kin.gz (1MB)  1dy5-cisTransPro.kin.gz (204KB)  rota4400-SerThrVal_3D.kin.gz (204KB)
Structures by NMR: assignment & worksheet:  HTML ||  222nmrWrksht.pdf (68KB)	Files for this lesson:  Xia.kin (148KB)  Hyberts.kin (120KB)  5ptiPaPb.kin (36KB)  Tendami.kin (352KB)