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Article title matches
- User:Angel Herraez/Sandbox 10 (360 bytes)
1: ...ing table of contentes when there is a StructureSection ==
3: __TOC__
5: == Function ==
9: == Structure ==
10: ...n load='1stp' size='340' side='right' caption='' scene=''> - User:Angel Herraez (3,444 bytes)
1: [[Image:Angel Herraez 01.jpg|right]]
2: Angel Herráez, PhD - Dept. of Systems Biology;
3: Biochemistry and Molecular Biology Unit;
4: [http://www.uah.es/ University of Alcalá], Spain
7: Not much info here, but you can visit - User:Angel Herraez/Sandbox 1 (491 bytes)
1: == Test for the sequence widget ==
4: ...ide='right' caption='initial scene from Karsten' scene='37/376372/Overall/3'>
5: Initial scene is a copy of User:Karsten_Theis/Showcase
7: ..._and_ligands/1'>1ea5, one chain with 2 ligands </scene>
9: ...me='33/337412/Dimer_cartoon/1'>hemoglobin dimer</scene> - User:Angel Herraez/Sandbox 2 (1,199 bytes)
7: <script>load =3cin</script>
11: These controls are inserted directly, as wiki extension tags:
13: <jmolCheckbox>
14: <scriptWhenChecked>spacefill on</scriptWhenChecked>
15: ...scriptWhenUnchecked>spacefill off</scriptWhenUnchecked> - User:Angel Herraez/Sandbox 3 (3,443 bytes)
1: ...ay of both evolutionary conservation and allosteric site ==
2: This is a proof-of-concept.
4: ...86' size='340' side='right' caption='Hemoglobin' scene=''>
7: ...ault_rendering/3'>default Proteopedia rendering</scene>
9: ...ndering/1'>Proteopedia rendering for Evol.Cons.</scene> - Image:Angel Herraez 01.jpg (98 bytes)
2: Provided by Angel Herraez
3: == Licensing ==
4: {{subst:Permission from license selector}} - User:Angel Herraez/Sandbox 4 (263 bytes)
2: ...ide='right' caption='Caption for this structure' scene=''>
6: </StructureSection> - User:Angel Herraez/Sandbox 5 (3,912 bytes)
2: ...js' side='right' caption='Dynein Light Chain 8a' scene=''>
5: ... in the asymmetric unit and dimeric in the biological assembly.
7: ...840/Cartoon_rainbow_and_water/1'>Color by group</scene>
9: ..._water/3'>without the water and a scene caption</scene>
11: ...st_characters/1'>Test of non-English characters</scene> - User:Angel Herraez/Sandbox 7 (1,250 bytes)
1: == Testing proposals for ligand focus ==
2: ...='right' caption='initial display of hemoglobin' scene=''>
4: ... start with a fresh reload of the dimer (asymmetric unit).
6: ...e same group name and focuses on their collective center.
10: ... ligand, <scene name='60/601886/Ligand_a/1'>HEM</scene> - User:Angel Herraez/Sandbox 8 (3,513 bytes)
3: ...This uses the inlineContents tag:
6: <color>#EEEEFF</color>
8: <inlineContents>
13: 0.6797 1.2651 -0.2387 C 0 0 0 0 0 0 0 0 0 0 0 0
14: 1.3944 -0.0096 0.2024 C 0 0 0 0 0 0 0 0 0 0 0 0 - User:Angel Herraez/Sandbox 6 (514 bytes)
2: ...ht' caption='Initial caption for this structure' scene=''>
4: == Extended ASCII characters ==
5: Testing externally made scenes
7: ...Gp120_domains_1/2">some gp120 domains and loops</scene>.
9: ...mains_1/3'>This is same scene but has a caption</scene>. - Category:Angel, T E (41 bytes)
1: List of pages with the keyword Angel, T E - Category:Angel, K C (41 bytes)
1: List of pages with the keyword Angel, K C - User:Angel Herraez/Sandbox 8b (541 bytes)
1: == Test of mmCIF assemblies ==
3: ...ide='right' caption='assembly of PDB entry 1xxx' scene=''>
7: The echo shows "simplifed model" -- OK
10: console
11: select protein and not alpha - User:Angel Herraez/Testing structure prediction (950 bytes)
1: ...ction load='' size='350' side='right' caption='' scene=''>
3: == Structure ==
6: ...e</scene> predicted via ESMFold for GenBank sequence AAW83741.1
8: ...e</scene> predicted via ESMFold for GenPept sequence 1HA8_A
10: ...xin_color_score/2'>Colored by reliability score</scene>. - User:Angel Herraez/Sandbox Advanced Scenes (1,395 bytes)
1: ...l renderings prepared outside Proteopedia into a scene ==
3: (For advanced users that are proficient in Jmol scripting out of Proteopedia)
5: ...or) and want to incorporate it in a Proteopediia scene, this is the way:
9: ... in the console, type <code>show state</code> and copy all the output.
10: ...ts <code>load /*file*/ </code> and delete it --or comment it out by prepending two slashes or a hash ... - User:Angel Herraez/Workbench (944 bytes)
2: Any subpages of the workbench subpage are also only visible to you as well as ...
4: ...very workbench page has a special workbench tab located on the top right side of the page.
5: ...ion special page, where you can manage the workbench page you started from.
6: ...hared Space with controlled restricted access for collaborative work.
9: ...e to you, give it a name that starts with "Workbench_" when you upload it. - User:Angel Herraez/Workbench/Ramachandran (6,092 bytes)
1: ...ngles (ϕ and ψ) in proteins and Ramachandran plot==
5: <th>Structure
7: ...px; text-align:center; display:inline-block;">Ramachandran plot</span>
11: <td style="padding-right:1ex; vertical-align:top;">
15: <color>white</color> - Image:Angel-2024-03.png (0 bytes)
- User:Angel Herraez/Sandbox 9 (311 bytes)
3: ...n load='1g3p' size='400' side='right' caption='' scene=''>
6: User:Tilman_Schirmer/Sandbox_99/Pro_213_in_cis_conformation/4
8: .../784289/Pro_213_in_cis_conformation/1'>cis bond</scene>
10: <scene name='78/784289/Using_rock/1'>rock</scene>
12: </StructureSection>
Page text matches
- Help:Editing (24,612 bytes)
1: <center><table style='background:#ffd8d8;' cellpadding='6'><tr><td>
2: Before using this page, you may find it useful to consult [[Proteopedia:Getting_Started|Help:Getting ...
3: </td></tr></table></center>
6: ...ia, as they have a much more complete help reference dealing with wikitext, and Proteopedia uses the ...
9: ==Use Sandboxes for practice editing== - 2c28 (5,240 bytes)
2: ...ihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4==
3: ...[[2c28]], [[Resolution|resolution]] 2.27Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2C28 FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.27Å</td></... - 2c2d (5,423 bytes)
2: ...ihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4==
3: ...[[2c2d]], [[Resolution|resolution]] 2.57Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2C2D FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.57Å</td></... - 2c2e (5,312 bytes)
2: ...ihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4==
3: ...[[2c2e]], [[Resolution|resolution]] 2.61Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2C2E FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.61Å</td></... - 2c2r (5,393 bytes)
2: ...ihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4==
3: ...[[2c2r]], [[Resolution|resolution]] 2.55Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2C2R FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.55Å</td></... - 2c22 (5,313 bytes)
2: ...ihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4==
3: ...[[2c22]], [[Resolution|resolution]] 2.56Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2C22 FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.56Å</td></... - 2jeg (5,678 bytes)
2: ... and X- Ray Crystallography of Correct and Incorrect Pairing==
3: ...[[2jeg]], [[Resolution|resolution]] 2.38Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2JEG FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.38Å</td></... - 2jej (5,601 bytes)
2: ... and X- Ray Crystallography of Correct and Incorrect Pairing==
3: ...[[2jej]], [[Resolution|resolution]] 1.86Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2JEJ FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.86Å</td></... - 2jef (5,668 bytes)
2: ...e and X-Ray Crystallography of Correct and Incorrect Pairing==
3: ...[[2jef]], [[Resolution|resolution]] 2.17Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2JEF FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.17Å</td></... - 2jei (5,601 bytes)
2: ... and X- Ray Crystallography of Correct and Incorrect Pairing==
3: ...[[2jei]], [[Resolution|resolution]] 2.39Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2JEI FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.39Å</td></... - 2bhk (9,039 bytes)
2: ...l structure of human growth and differentiation factor 5 (GDF5)==
3: ...[[2bhk]], [[Resolution|resolution]] 2.40Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2BHK FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4Å</td></t... - 2bq3 (5,459 bytes)
2: ...Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine==
3: ...[[2bq3]], [[Resolution|resolution]] 2.00Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2BQ3 FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> - 2bqr (5,535 bytes)
2: ...Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine==
3: ...[[2bqr]], [[Resolution|resolution]] 2.37Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2BQR FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.37Å</td></... - 2bqu (5,538 bytes)
2: ...Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine==
3: ...[[2bqu]], [[Resolution|resolution]] 2.50Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2BQU FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></t... - 2uvr (5,202 bytes)
2: ...with 8-oxoG containing DNA template-primer constructs==
3: ...[[2uvr]], [[Resolution|resolution]] 2.90Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2UVR FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9Å</td></t... - 2uvv (5,202 bytes)
2: ...with 8-oxoG containing DNA template-primer constructs==
3: ...[[2uvv]], [[Resolution|resolution]] 2.20Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2UVV FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></t... - 2uvw (5,203 bytes)
2: ...with 8-oxoG containing DNA template-primer constructs==
3: ...[[2uvw]], [[Resolution|resolution]] 2.09Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2UVW FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.09Å</td></... - 2uvu (5,202 bytes)
2: ...with 8-oxoG containing DNA template-primer constructs==
3: ...[[2uvu]], [[Resolution|resolution]] 2.70Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2UVU FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7Å</td></t... - 1waq (9,682 bytes)
2: ...l structure of human Growth and Differentiation Factor 5 (GDF-5)==
3: ...[[1waq]], [[Resolution|resolution]] 2.28Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=1WAQ FirstGlance]. <br>
6: ...><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.28Å</td></... - 2br0 (5,203 bytes)
2: ...Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine==
3: ...[[2br0]], [[Resolution|resolution]] 2.17Å' scene=''>
4: == Structural highlights ==
5: ...s://proteopedia.org/fgij/fg.htm?mol=2BR0 FirstGlance]. <br>
6: ...ene name='pdbligand=GNE:1,N2-ETHENOGUANINE'>GNE</scene></td></tr>
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