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- FirstGlance in Jmol Literature Citations (30,325 bytes)
1: ...), and all were verified to cite ''FirstGlance in Jmol''.
3: [[FirstGlance in Jmol]] offers, since 2006, free visualization and anal...
4: * [[FirstGlance in Jmol]]
5: ....htm#unique Unique Capabilities of FirstGlance in Jmol]
7: ...Index]], a list of resources about FirstGlance in Jmol, including all the relevant pages in Proteopedia. - User:Jaime Prilusky/Test/Jmol versions (1,239 bytes)
23: ... Compare to rendering with the default version of Jmol (14.31.8) - Image:Sticks jmol.png (0 bytes)
- Image:New Surface Bonds Jmol.png (0 bytes)
- Sandbox Jmol Jane (1,030 bytes)
2: ...on='Caption for this structure' scene='10/1081074/Jmol_jane_1eve/1'>
3: This is a default text for your page '''Sandbox Jmol Jane'''. Click above on '''edit this page''' to m...
4: ...ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
7: <scene name='10/1081074/Jmol_jane_1eve/1'>Jmol_Jane_1eve</scene> - Image:2H5I Dimer.jmol (0 bytes)
- Jmol/Cavities pockets and tunnels (22,245 bytes)
2: Jmol can find and display cavities, pockets, and tunne...
8: ...e generated in the [[Jmol/Application|stand-alone Jmol application]] and captured "cached" in a PNGJ fil...
11: Jmol uses two "rolling" spherical probes to identify c...
20: The simplest Jmol cavity command is
28: ...d error, a good minset number is 1000, making the Jmol command: - Image:012 3b jmol 16 2 450 450.png (0 bytes)
- Image:Fig 03c jmol 14p31p8.png (0 bytes)
- Image:Fig 03c jmol 14p31p8 450.png (0 bytes)
- Image:Fig 03c jmol 14p31p8 white 450 center.png (0 bytes)
- Image:Fig 03a jmol 16 2 21 450 center wireframe spacefill.png (0 bytes)
- Image:012 2a jmol 16 3 450 450.png (0 bytes)
- Image:012 2c jmol 16 3 450 450.png (0 bytes)
- Image:012 3c jmol 14 450 450.pngj (0 bytes)
- Image:012 3c jmol 16 3 450 450.pngj (0 bytes)
- Image:2hhd jmol state test.gif (86 bytes)
1: Snapshot of Jmol 11.5.35 from which state script was obtained, see... - FirstGlance in Jmol (5,275 bytes)
2: ...ot of [http://firstglance.jmol.org FirstGlance in Jmol]]]
3: ...L]], [[ChimeraX]], or [[Mol*]] offered by the [[wwPDB]].
5: ...l], you can enter any [[PDB code]], or upload a [[PDB file]] from your computer, such as a prediction b...
7: ...ules tinyurl.com/movingmolecules]. FirstGlance in Jmol version 4.0 was released August 15, 2022, with ne...
9: ...s from menus and forms -- no familiarity with the Jmol command scripting language is required. Tooltips ... - Jmol (17,388 bytes)
1: ...ks]]. An overview of other Jmol resources is at [[Jmol/Index]].
5: ...[User:Eric_Martz/JSmol_Notes#JSmol_is_slower_than_Jmol|performs much faster]], but this enhanced perform...
14: ==Jmol Has Two Forms==
43: Proteopedia, [[FirstGlance in Jmol]], [http://molviz.org MolviZ.Org],
50: OBSOLETE <font color="red"><b>Jmol_S</b></font> (in web browser) - User:James D Watson/Using Jmol (11,635 bytes)
1: ==Introduction to Jmol==
2: Jmol is a commonly used molecular graphics viewer. The...
4: ...for you to interact with protein structures using Jmol:<UL>
30: ...s section, we will represent selections using the Jmol menu in '''''this style'''''.<br/>
37: ...globin molecule' scene='User:James_D_Watson/Using_Jmol/Haemoglobin_start/1'/>
Page text matches
- Help:Editing (24,612 bytes)
46: ...et are in the next section below. When there is a Jmol structure applet present in the page, you create ...
50: When there is more than one Jmol structure applet on a page, scenes automatically ...
52: ==Proteopedia Jmol Structure Applets==
53: ...the molecular scene. The wikitext for inserting a Jmol structure applet must be entered on the page foll...
55: : <nowiki><Structure load='Insert PDB code or filename here' size='X' frame='X' align='... - Peptide (2,365 bytes)
18: ...emoglobin Hemoglobin Tutorial] implemented with [[Jmol]] in July 2007. - CHEM2052 Tutorial (6,397 bytes)
1: ..._chymotrypsin-triad/2' caption='α-chymoptrypsin (PDB code [[2cha]])'>
15: ...he structure. Alternatively, you can click on the Jmol symbol in the lower right-hand corner of each ima...
18: ...ript><text>Click this button</text></jmolButton></jmol> to flip between structures.
38: == '''Additional PDB Structures''' == - Help:Contents (6,518 bytes)
14: ... a window integrated into the page (often called "Jmol window"). As you read through the text of an entr...
38: ...ols]]. If you want to show a structure not in the PDB, you have to upload the structure first ([[Help:U...
49: ...ails, see [[Jmol/Interactivity]]). Consult [[Help:Jmol]] for advanced 3D scenes. To look under the hood ... - Proteopedia:About (7,060 bytes)
31: ...ft, usually you will get an article titled with a PDB code, since they outnumber human-authored article...
34: ...s/a | complete list of articles not titled with a PDB identification code]]. There are also articles [[...
43: ...eopedia:Team|Proteopedia team]]. The [http://wiki.jmol.org/ JSmol object] is used to render the rotatabl...
50: ...l]] have been made what they are today by [http://jmol.sourceforge.net/history/ many dedicated volunteer... - Scene authoring tools (23,035 bytes)
6: ...T. In this case, first edit the page to include a Jmol window (using the [[Image:Structure buttons.JPG|5...
11: Insert PDB code or filename here' size='350' frame='true' al...
18: ...s that someone viewing the page can load into the Jmol viewer by clicking on green links. A scene store...
30: ..., while the right side of the user interface is a Jmol viewer to preview the scene as it is built.
36: ... load molecule tab is used to load molecules into Jmol. - User:Karsten Theis/Linear interpolation (911 bytes)
1: This is a Jmol script that does linear interpolation. You need t...
18: To try it, right-click in the Jmol window to open the console, and then copy and pas... - User:Karsten Theis/Rigid body interpolation (4,709 bytes)
1: ...erform supoerpositions and to create morph, see [[Jmol/Storymorph]].
113: ... the following three lines while running in local Jmol app
114: // fname = "morph" + i + ".pdb" - User:Anna Leibinger/Sandbox 1 (11,577 bytes)
2: ...ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the --[[User:Anna Lei... - Art:Cytochrome Wallpaper (391 bytes)
6: ... was generated from [[1os6]] with the following [[Jmol]] command script: <br><pre>
16: [[Category: PDB Art]] - FirstGlance in Jmol Literature Citations (30,325 bytes)
1: ...), and all were verified to cite ''FirstGlance in Jmol''.
3: [[FirstGlance in Jmol]] offers, since 2006, free visualization and anal...
4: * [[FirstGlance in Jmol]]
5: ....htm#unique Unique Capabilities of FirstGlance in Jmol]
7: ...Index]], a list of resources about FirstGlance in Jmol, including all the relevant pages in Proteopedia. - User:Wayne Decatur/UNH BCHEM833 Structural Analysis Workshop Session Fall 2012 (17,130 bytes)
16: **Have a PDB id for a pertinent structure?
23: ...er considered for not highlighting in Proteopedia PDB entry pages.</small>
28: ...pplications_Embedding_Jmol Applications Embedding Jmol] for many more
30: **FirstGlance in Jmol (adopted by Nature <nowiki>[</nowiki>example [htt...
31: ....org/index.php/Journals_Using_Jmol Journals Using Jmol] for more - User:Chloe Tucker/Sandbox 1 (4,378 bytes)
4: ...ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. - Teaching Scenes, Tutorials, and Educators' Pages (12,171 bytes)
63: ...ludes instructions for using Jmol commands in the Jmol console for advanced scene authoring.
144: ...e [[:Category:RCSB_PDB_Molecule_of_the_Month|RCSB PDB Molecule of the Month]].
155: <td>[http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_06 Vaults]</td>
160: <td>[http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_05 Influenza Neuraminidase]</td>
165: <td>[http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_04 Oct and Sox Transcription Factors]</t... - Missing residues and incomplete sidechains (25,887 bytes)
4: ... and [[cation-pi interactions]]. [[FirstGlance in Jmol]] makes it less likely, compared to other popular...
6: ...RCSB].</ref> of the [[Empirical models]] in the [[PDB]], some residues (amino acids or nucleotides) tha...
18: ... consider [[Renumbering PDB files|renumbering the PDB file]].
22: Unlike other viewers, [[FirstGlance in Jmol]] ensures that you are aware of missing ends by m...
90: ...e.jmol.org/fg.htm?mol=2ace 2ace in FirstGlance in Jmol] - User:Jaime Prilusky/Test/Jmol versions (1,239 bytes)
23: ... Compare to rendering with the default version of Jmol (14.31.8) - Sandbox 16p3p1 (939 bytes)
4: ...ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. - User:Clara Fernández Vidal/sandbox1 (955 bytes)
5: ...ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. - Sandbox Muzic (1,567 bytes)
4: ...ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
12: ! PDB ID !! Structure !! PubMed link - Sandbox I3DC 001 (941 bytes)
4: ...ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
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