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  1. Scene authoring tools (23,035 bytes)
    1: ...for creating a molecular scene with Proteopedia's Scene Authoring Tools]], and watch the introductory vid...
    3: ==Where are the ''Scene authoring tools''?==
    6: ...''. Click on '''show''' to expand and open the ''Scene authoring tools''. If, however, the page does not...
    11: ...tion='Insert caption here' scene='Insert optional scene name here' />
    16: ...for creating a molecular scene with Proteopedia's Scene Authoring Tools]] for tutorial examples.
  2. Image:Cavitycompare1 scene 1.min.pngj (26 bytes)
  3. Image:Cavitycompare2 scene 1.all.pngj (26 bytes)
  4. Image:Cavitycompare2 scene 1.min.pngj (26 bytes)
  5. Image:Cavitycompare1 scene 1.all.pngj (26 bytes)
  6. Sandbox scene (708 bytes)
    6: ...עוני של המוגלובין' scene='Sandbox_scene/Start/1' />
    9: .../1'>קבוצות ההם על רקע החלבון</scene>
    11: ...'>קבוצות ההם בלבד ללא חלבון</scene>
    13: ...dbox_scene/Start/1'>חזרה למודל המלא</scene>
  7. Image:Inhibitors1 scene 4.all.pngj (26 bytes)
  8. Image:Inhibitors1 scene 4.min.pngj (26 bytes)
  9. Image:Cavitycompare1 scene 2.all.pngj (26 bytes)
  10. Image:Cavitycompare1 scene 2.min.pngj (26 bytes)
  11. Image:Cavitycompare2 scene 2.all.pngj (26 bytes)
  12. Image:Cavitycompare2 scene 2.min.pngj (26 bytes)
  13. Image:1A2 scene 1.pngj (0 bytes)
  14. Image:1A2 scene 1.spt.pngj (0 bytes)
  15. Image:1A2 scene 2.pngj (0 bytes)
  16. Image:1A2 scene 2.spt.pngj (0 bytes)
  17. Image:1A2 scene 3.pngj (0 bytes)
  18. Image:1A2 scene 3.spt.pngj (0 bytes)
  19. Image:ArtPage scene 3.all.pngj (0 bytes)
  20. Image:ArtPage scene 3.min.pngj (0 bytes)

Page text matches

  1. Help:Editing (24,612 bytes)
    15: If you plan to edit the text or the molecular scenes in an existing page, you can skip this section. ...
    45: ==<big>To create or edit Proteopedia Scenes</big>==
    46: ...sert it using the appropriate wikitext that the ''Scene Authoring Tools'' will generate for you.
    48: '''SCENE TUTORIAL MOVIE:''' There is a video tutorial avai...
    50: ...o to the applet above the <nowiki><scene ...>...</scene></nowiki> tag in the wikitext.
  2. Matrix metalloproteinases (1,425 bytes)
    2: {{STRUCTURE_2clt| PDB=2clt | SIZE=300| SCENE=Matrix_metalloproteinase/Cv/1 |right| CAPTION= ...
  3. Hemoglobin (19,234 bytes)
    1: ...rystallographic structure of HbII- oxy [[3P31]]" scene="Hemoglobinits/5" >
    9: ... <scene name='Hemoglobin/4heme/3'>heme molecules</scene> give hemoglobin its red color.
    11: ...in/Oxysubunitsf/4'>oxygenated heme group is held</scene> within the polypeptide.
    13: ...'Hemoglobin/Anchortrace/5'>Anchoring of the heme</scene> is facilitated by a histidine nitrogen that bind...
    15: ...32/Hemoglobins_1hho/9'>glutamic acid to a valine</scene>. This hemoglobin variant is termed 'hemoglobin ...
  4. Ann Taylor/Hemoglobin (7,712 bytes)
    1: ... chain (green and yellow) with bound O2 [[1gzx]]" scene="Hemoglobin/1gzx/2" >
    2: ... <scene name='Hemoglobin/4heme/3'>heme molecules</scene> give hemoglobin its red color.
    4: ...me='57/576710/Oxy_fe_planarity/3'>into the plane</scene> of the heme.
    6: ...bin structure and vice versa. Remember that this scene shows a subunit in the all-unliganded versus the ...
    11: ...7/576710/Glu_to_val/1'>glutamic acid to a valine</scene>. This hemoglobin variant is called 'hemoglobin ...
  5. Help:Contents (6,518 bytes)
    14: ...arn how to get the most out of the interactive 3D scenes, reference the [[Help:Viewing pages|Viewing guid...
    37: ...lass="fas fa-cubes"></i> For authors: creating 3D scenes===
    38: ...stand is available at [[Proteopedia:How to Make a Scene]].
    45: ... embed videos, and integrate different data in 3D scenes, see [[Help:Multimedia]]. Proteopedia hosts imag...
    49: ...ages, use the "edit this page" tab. [[Proteopedia:DIY:Templates|Templates]] and [[Proteopedia:Macros|m...
  6. Proteopedia:About (7,060 bytes)
    43: ... to render the rotatable, zoomable macromolecular scenes. <!--The [http://kinemage.biochem.duke.edu/softw...
  7. Scene authoring tools (23,035 bytes)
    1: ...for creating a molecular scene with Proteopedia's Scene Authoring Tools]], and watch the introductory vid...
    3: ==Where are the ''Scene authoring tools''?==
    6: ...''. Click on '''show''' to expand and open the ''Scene authoring tools''. If, however, the page does not...
    11: ...tion='Insert caption here' scene='Insert optional scene name here' />
    16: ...for creating a molecular scene with Proteopedia's Scene Authoring Tools]] for tutorial examples.
  8. Sandbox 781 (8,140 bytes)
    3: ...me='61/612822/Asymmetric_unit/1'>asymmetric unit</scene> ((6OYH))' size='340' side='right' caption='Cryst...
    13: ...42/421575/Carbacaprazamycin/1'>Carbacaprazamycin</scene> is a chemically stable analog of caprazamycin nu...
    24: ...me='61/612822/Asymmetric_unit/1'>asymmetric unit</scene>, which contains 4 biological units of MraYAA (co...
    28: ... Asp118 which are involved in Mg2+coordination</scene> <ref name="four">PMID:29438582</ref>.TM5–TM10...
    30: ...21575/Binding_site/1'> T75, N190, D193, and G264</scene>, called the uridine-adjacent pocket. The 5-amino...
  9. Sean Swale/Human Thrombin Inhibitor (6,165 bytes)
    2: {{STRUCTURE_3utu| PDB=3utu | SIZE=400| SCENE= |right|CAPTION=Human Thrombin, heavy chain (red)...
    4: ...Human_Thrombin_Inhibitor/Active_site/3'>Thrombin</scene> Inhibitor===
    5: ..._Thrombin_Inhibitor/Inhibitor_65/1'>inhibitor 65</scene>.<ref> DOI: 10.1002/cmdc.201200292</ref>
    12: ...e/Human_Thrombin_Inhibitor/P2_proline/1'>proline</scene> residue is in another hydrophobic pocket made up...
    18: ...an_Thrombin_Inhibitor/P3_binding_site/6'>residue</scene>, there the backbone of asparagine forms and anti...
  10. 9ith (9,207 bytes)
    3: ...'[[9ith]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
    7: ... name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
    11: ...e of a complete autopsy, examination of the death scene, and review of clinical history. Pathophysiologic...
  11. User:Anna Leibinger/Sandbox 1 (11,577 bytes)
    137: ...cratch or loading and editing one of these sample scenes.
  12. User:Juliette Personius/sandbox 1 (7,068 bytes)
    1: ...x_1/Tyrosines_1349_and_1356/1'>TextToBeDisplayed</scene>===Hepatocyte Growth Factor Receptor c-Met===
    8: {{STRUCTURE_1r1w| PDB=1r1w | SCENE= }}
    10: ...49_and_1356/1'>tyrosine residues (1349 and 1356)</scene> . Studies with mice have shown that these tyrosi...
    11: ...te_Personius/sandbox_1/Beta_sheets/2'>β-sheets </scene> and is linked through a hinge to the C lobe, whi...
    15: {{STRUCTURE_1r0p| PDB=1r0p | SCENE= }}
  13. User:Juliette Personius/Sandbox 1 (90 bytes)
    1: {{STRUCTURE_1r0p| PDB=1r0p | SCENE= }}
  14. User:Valentine J Klimkowski/Sandbox 99 (1,300 bytes)
    2: ...tion='Insert caption here' scene='Insert optional scene name here' />
    4: <scene name='10/1040145/7tyf_init/2'>7tyf_init</scene>
    6: ... name='10/1040145/7tyf_removess/2'>7tyf_removeSS</scene>
    8: ...f-7tyy-7tyf_aligned/1'>aligned imported together</scene>
    9: ...ne name='10/1040145/7tyy-aligned/1'>7tyy-aligned</scene>
  15. User:Jaime Prilusky/Test/SAT Molstar (3,477 bytes)
    1: ...' size='340' side='right' caption='initial scene' scene='83/839292/1cbs_experimental_data/1'>
    3: ...name='83/839292/1cbs_experimental_data/1'>initial scene</snapshot> as examples. Also, you may use <snaps...
    33: ...cene name='83/839292/corona/1'>should be ignored</scene>
    45: <scene>83/839292/Test/4</scene>
  16. Wittman Gal4 Sandbox (1,419 bytes)
    3: {{STRUCTURE_1d66| PDB=1d66 | SCENE= }}
  17. User:Wayne Decatur/UNH BCHEM833 Structural Analysis Workshop Session Fall 2012 (17,130 bytes)
    98: **Jmol in FirstGlance or Jmol via Proteopedia's Scene Authoring Tools:
    105: ...[[1d66]] in [[Scene authoring tools|Proteopedia's Scene Authoring Tools]]
    133: ==Proteopedia Scene Authoring==
    134: *[[Scene authoring tools|Proteopedia's Scene Authoring Tools]]
    135: **Load a structure [[1d66]] or previous scene
  18. Sandbox Reserved 703 (6,062 bytes)
    5: {{STRUCTURE_2v3q| PDB=2v3q | SCENE= }}
    23: ... size='400' frame='true' align='right' caption='' scene='' />
    25: ...Sandbox_Reserved_703/Disulfid_bond2/1'>C306-C369</scene>).
    27: ...Sandbox_Reserved_703/Active_site1/1'>active site</scene> is similar to other phosphate SBPs and the surfa...
    28: ...ins <scene name='Sandbox_Reserved_703/Ohs/1'>OHs</scene> of 4 residues (T8, S32, S144, T146).
  19. User:Chloe Tucker/Sandbox 1 (4,378 bytes)
    2: ...340' side='right' caption='GIP with GIP receptor' scene='10/1038815/Overview/1'>
    17: ...cratch or loading and editing one of these sample scenes.
    20: ...<scene name='10/1038815/Overview/7'>binding site</scene> of GIP with the GIP receptor (GIPR) is where the...
    21: ... <scene name='10/1038815/Active_site/3'>residues</scene> within the binding site are forming hydrogen bon...
    25: ...ame='10/1038815/Tirzepatide_residues/7'>residues</scene> are fairly similar just in a different conformat...
  20. Emily Ellis/Sandbox (4,365 bytes)
    10: <StructureSection size='340' side='right' scene='61/611451/Mirror_image/2'>
    14: ... <scene name='61/611451/Salbutamol/5'>green link</scene>, we'll show the actual drug in the browser as we...
    32: ...11451/Adrenergic_receptor/6'>adrenergic receptor</scene>.
    34: ...='61/611451/Adrenergic_receptor/7'>all the atoms</scene>. Use the links below to "shave away" parts of th...
    52: The next scene shows salbutamol in red, and those parts of the r...

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