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1. User:Karsten Theis/Linear interpolation (911 bytes)
   1: ...conformation or position). Here, I am using residues 5 and 6 of 1BNA.
   6: five = {5}.xyz.all
   8: interp = six
   9: progress = 0.5
   10: ssergorp = 1 - progress
2. User:Karsten Theis/Rigid body interpolation (4,709 bytes)
   1: ...to perform supoerpositions and to create morph, see [[Jmol/Storymorph]].
   3: ... anchor (center of mass, given atom) is in the same location.
   5: ...ms in the same order, but with different coordinates.
   9: ...olation of coordinates in the atom sets sel1 and sel2
   10: ...t} sel1 First set of atoms, will be modified by the function
3. Image:Karsten-2024-03.png (0 bytes)
4. User:Karsten Theis/Showcase (4,137 bytes)
   1: == Proteopedia and Biomolecular Visualization ==
   4: ...='350' side='right' caption='' scene='37/376372/Overall/3'>
   6: ...lycine/Emartz_ballandstick/1'>ball and stick</scene>
   7: ...scene name='78/786673/Gal_overal_view/1'>GAL</scene>
   8: === Access ===
5. User:Karsten Theis/Sandbox 6 (834 bytes)
   1: https://www.frontiersin.org/articles/10.3389/fmicb.2020.02014/full
   2: Size comparison human cell and coronavirus
   4: Outline
   5: ...(Virus vs Bacterium), chronic diseases, other causes
   6: * Size of protein, virus, human cell
6. User:Karsten Theis (3,127 bytes)
   1: ...mical and Physical Sciences], Westfield State University
   4: ...ch Interests: Chemistry education, DNA repair, molecular motors, X-ray crystallography
   7: ...ademics/chemistry-degrees/faculty-staff/karsten-theis]
   12: ...impact structures]] (I added the bit about lysozyme in 2008)
   13: ...Feb 2010 version]], used for my job talk at Westfield that month)
7. User:Karsten Theis/Animation course (20,085 bytes)
   1: ...de='right' caption='' scene='52/520489/Ligand_pocket/2'>
   3: ==Animate a scene with Jmol==
   5: ===Load the scene and choose a look===
   6: ...</text></jmolLink></jmol> and try different representations and colors.
   8: 1. Choose a background:
8. User:Karsten Theis/transition proposal (2,998 bytes)
   1: ...de='right' caption='UvrB in complex with ATP' scene='77/779435/Front/1'>
   2: ...ferent parts of a structure without losing their bearing.
   4: ==Proposal: smooth transition as default==
   6: ...re reloaded, show the new scene as fast as possible.
   8: ...oading a scene. This slows down browsing the figures.
9. Karsten Theis sandbox 1 (13,880 bytes)
   1: {{BAMBED
   2: |DATE=August 20, 2011
   4: |BAMBEDDOI=10.1002/bmb.20566
   7: ...l instructions for the development, survival and reproduction of organisms.
   8: ...ref name='gene'>http://www.genome.gov/25520880 </ref>
10. User:Karsten Theis/overall views (19,556 bytes)
    3: <gallery>
    4: Image:UvrB fold.JPG
    5: Image:UvrB charge.JPG
    6: Image:UvrB slab core.JPG
    7: Image:UvrB consurf.JPG
11. User:Karsten Theis/Textbook supplement (32 bytes)
    1: #REDIRECT [[Biochemistry in 3D]]
12. User:Karsten Theis/Sandbox 1 (2,033 bytes)
    1: <applet size='[450,338]' frame='true' align='right'
    2: scene='User:Karsten_Theis/Sandbox_1/Globe3/2'
    7: ...can rotate around its single bonds to get a different conformation:
    11: ...; rotate branch {C3}{C2} 2; set refreshing true; delay 0.05}}
    13: <text>rotate</text>
13. User:Karsten Theis/Sandbox 3 (9,590 bytes)
    1: == Proteopedia annotated bibliography ==
    4: https://www.learntechlib.org/p/35558/
    5: ...etrieved February 20, 2021 from https://www.learntechlib.org/primary/p/35558/.
    7: Unfolding Proteins
    8: Maura C. Flannery
14. User:Karsten Theis/Sandbox 2 (0 bytes)
15. User:Karsten Theis/Physical Models (841 bytes)
    1: ==3D printed models==
    3: ...ggregation and protein stability aided by disulfide bonds.
    5: ... stage. Nevertheless, here are links to each of them:
    7: *Antibodies: [[User:LeeAnne Brown/Sandbox 1]]
    8: *Amyloid beta fibrils:[[User:Kaeleigh Chartrand/SANDBOX]]
16. Category:Karsten, W E (43 bytes)
    1: List of pages with the keyword Karsten, W E
17. User:Karsten Theis/polymerase (68 bytes)
    1: ...NAP_transition_sketch.png]][[Image:Ezgif.com-resize.gif]]
18. Category:Karsten, S (41 bytes)
    1: List of pages with the keyword Karsten, S
19. User:Karsten Theis/Chymotrypsin (2,744 bytes)
    1: ...on load='' size='350' side='right' caption='' scene='Chymotrypsin/Chymotrypsin_triad/2'>
    3: ...xt and watch how the 3D picture on the right changes.
    4: ==Overview==
    6: ... processes relevant to human health and agriculture.
    8: ... In its mature form, bovine chymotrypsin is a protein consisting of 245 amino acids. This string of a...
20. User:Karsten Theis/Chymotrypsins (45 bytes)
    1: #REDIRECT [[User:Karsten Theis/Chymotrypsin]]

Page text matches

1. Image:DHFR 3dfr 1dls.pdb (175 bytes)
   2: ...s (human DHFR) with ligands NDP and MTX superimposed
   3: REMARK Karsten Theis 1/8/2022
   4: == Licensing ==
   5: {{self|cc-by-sa-3.0|GFDL}}
2. 1o0s (4,330 bytes)
   2: ...tal Structure of Ascaris suum Malic Enzyme Complexed with NADH==
   3: ...o0s]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
   5: ...://proteopedia.org/fgij/fg.htm?mol=1O0S FirstGlance]. <br>
   6: ..." id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
   7: ..., <scene name='pdbligand=TTN:TARTRONATE'>TTN</scene></td></tr>
3. User:Karsten Theis/Showcase (4,137 bytes)
   1: == Proteopedia and Biomolecular Visualization ==
   4: ...='350' side='right' caption='' scene='37/376372/Overall/3'>
   6: ...lycine/Emartz_ballandstick/1'>ball and stick</scene>
   7: ...scene name='78/786673/Gal_overal_view/1'>GAL</scene>
   8: === Access ===
4. Proteopedia:Wishlist (29,517 bytes)
   1: ... try to implement the best and most appropriate ideas.
   3: ...sting feature, please do so at [[Proteopedia:Problems]].
   5: ...itext that is converted into your name and the date.
   7: ...Please insert your wish after items that seem higher in priority.
   9: ==Wishlist for Outside the [[SAT|Molecular Scene Authoring Tools (SAT)]]==
5. Resolution (14,174 bytes)
   1: <table align="right" border="0" width="200"><tr><td>
   2: [[Image:Resolution-holton-5.0.png]]
   4: [[Image:Resolution-holton-3.5.png]]
   6: [[Image:Resolution-holton-2.5.png]]
   8: [[Image:Resolution-holton-1.4.png]]
6. Morphs (23,799 bytes)
   1: ...ressor#Specific Binding|Details]].</td></tr></table>
   2: ... an animation showing a transition between two molecular conformations.
   3: ==Examples of Morphs==
   5: ===Morphs in Proteopedia===
   7: * Coronavirus: [[SARS-CoV-2 spike protein fusion transformation]], a morph animation.
7. User:Karsten Theis (3,127 bytes)
   1: ...mical and Physical Sciences], Westfield State University
   4: ...ch Interests: Chemistry education, DNA repair, molecular motors, X-ray crystallography
   7: ...ademics/chemistry-degrees/faculty-staff/karsten-theis]
   12: ...impact structures]] (I added the bit about lysozyme in 2008)
   13: ...Feb 2010 version]], used for my job talk at Westfield that month)
8. Proteopedia:Team (2,499 bytes)
   1: ==The Proteopedia Team==
   2: ===Proteopedia Founders & Developers===
   3: <gallery perrow="3">
   4: ...ser:Jaime_Prilusky|Jaime Prilusky]]<br>'''Co-Founder'''
   5: ....png|[[User:Eran_Hodis|Eran Hodis]]<br>'''Co-Founder'''
9. Temperature value (12,001 bytes)
   1: ...acromolecular Crystallography] at ProXyChem.com</ref>.
   3: ... is a common way to visualize the uncertainty for each atom.
   5: ...all analyzed cryo-EM models"<ref>PMID: 28867613</ref>.
   8: ==Definition==
   9: ...rature value, B factor, B value'', or ''Debye-Waller factor'') is
10. Electron density maps (12,314 bytes)
    1: ...//www.bioinformatics.org/molvis/edm/ Interactive Version]]]
    2: ...of the macromolecular structures available from the
    3: [[Protein Data Bank]] (PDB)
    4: were determined by
    5: ...ar model reveals regions of uncertainty in the model.
11. Ubiquitin Structure & Function (9,224 bytes)
    1: ...='right' caption='Human ubiquitin, [[1ubq]])' scene=''>
    3: ... degradation<ref name="mainpaper">PMID: 3041007</ref>
    7: ...uitin found in higher eukaryotes<ref name="mainpaper"/>.
    8: ...n structure: Arg74 in pink and Gly75 Gly76 in white.]]
    10: ... content below was inserted by the ConSurf template -->
12. Proteopedia:Scrapbook (5,944 bytes)
    1: ... about Proteopedia, its dissemination and development.
    3: ==Proteopedia People==
    4: ...ut upgrading the infrastructure of Proteopedia were:
    5: {| class="wikitable"
    6: |[[Image:Jaim-2024-03.png|150px]]
13. Thymidylate synthase (8,831 bytes)
    1: ...ame="Kholodar" >DOI:10.1021/acs.biochem.1c00063</ref>
    3: ... thymidine 5'-monophosphate(dTMP) + Dihydrofolate(H₂F)
    5: [[Image:TS Overview.jpg|1000px]]
    7: ... the substrates and products as a result of this reaction.
    9: ...structure. The TS ThyX are flavin-dependent enzymes.
14. Jmol/Using the console (4,640 bytes)
    1: ...via a dedicated button under the Jmol window in the SAT.
    2: ...on load='' size='340' side='right' caption='' scene='86/865284/Myoglobin/1'>
    5: ...ipt></jmolButton></jmol><div id=JmolApplet0_console></div>
    7: show sequence
    9: This shows the residues that contain selected atoms
15. Image:Proteopedia rubrics.pdf (113 bytes)
    2: ...good pages and good figures, written by Karsten Theis
    3: == Licensing ==
    4: {{self|cc-by-3.0}}
16. Carbohydrate (726 bytes)
    1: ...ata/exploring-carbohydrates-in-the-pdb-archive here].
    3: * [[Disaccharides]]
    4: * [[Hexoses]]
    5: * [[Polysaccharides]]
    7: ...on carbohydrates as a family or on specific examples
17. Proteopedia:I3DC (78,583 bytes)
    1: __NOEDITSECTION__
    2: === Acta Cryst D ''Acta Crystallographica Section D: Biological Crystallography'' ===
    3: https://proteopedia.org/logos/small/Acta_Cryst_D.png
    4: ... Iva Necasova, Petr Cech, Daniel Svozil and Jiri Cerny [https://dx.doi.org/10.1107/S2059798318000050 ...
    5: ...sten Andersen, Keith S. Wilsona and Gideon J. Davies [https://dx.doi.org/10.1107/S2059798318014900 ht...
18. Methionine adenosyltransferase (7,366 bytes)
    1: ...een shown to cause diseases including various cancers.
    3: == Relevance ==
    4: ...s related in alteration in MAT<ref>PMID:7741002</ref>.
    7: == Function and reaction mechanism ==
    8: ...are Mg+2 (or Co+2) and K+ ions<ref>PMID:8611562</ref>.
19. Category:Karsten, W E (43 bytes)
    1: List of pages with the keyword Karsten, W E
20. Image:Fibril chains.pdb (376 bytes)
    2: ... selecting 18 chains and adding chain IDs for easier visualization
    4: ...nt according to https://www.frontiersin.org/articles/10.3389/fpls.2020.00479/full
    6: ...ose builder described in https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.22959
    8: == Licensing ==
    9: {{self|cc-by-3.0}}

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