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1. Image:Arg mutation file.pdb (0 bytes)
2. Atomic coordinate file (9,130 bytes)
   3: Atomic coordinate files are the data files that specify three-dimensional (3D) molecular st...
   7: ...tp://openbabel.org/wiki/XYZ_(format) XYZ format] (file type .xyz) specifies only the coordinates and che...
   9: Macromolecular atomic coordinate files need to specify quite a bit of information in ad...
   13: ...tions, it remains popular partly because the data files are in plain text, and are relatively easy to re...
   15: ...provides the [https://www.wwpdb.org/documentation/file-format complete description of the final PDB form...
3. PDB file format (36 bytes)
   1: #REDIRECT [[Atomic coordinate file]]
4. PDB file (36 bytes)
   1: #REDIRECT [[Atomic coordinate file]]
5. Image:FILE consurf1243922409 pipe.pdb (0 bytes)
6. Image:FILE consurf1240241051 pipe.pdb (0 bytes)
7. Image:FILE consurf1240240806 pipe.pdb (0 bytes)
8. Image:FILE consurf1254065510 pipe.pdb (33 bytes)
9. Help:Modify A PDB File (2,390 bytes)
   1: This page explains some ways to modify a PDB file in order to use it to show what you want to show.
   3: ==Merging two (or more) PDB files==
   4: ...ave your resulting multi-model or multi-chain PDB file, upload it into Proteopedia, and then load it in ...
   6: ...aving the same chain name in the resulting merged file.
   7: # load the PDB files into PyMOL and align them if desired (align by c...
10. Image:Pdb file diagram.png (0 bytes)
11. Testing PDB File Sizes (3,489 bytes)
    10: ! file size from OCA
    246: ....weizmann.ac.il/oca-docs/PDBSizeDistribution.html File size Distribution of PDB entries from OCA ] with ...
    247: ...ed here] for a plot based on the current table of File size Distribution of PDB entries from OCA.
12. Pdb file (36 bytes)
    1: #REDIRECT [[Atomic coordinate file]]
13. Image:Upload file.png (0 bytes)
14. Image:ASGR1 homology model PDB file.pdb (85 bytes)
15. Image:ASGR1 homology model PDB file.pdb.gz (85 bytes)
16. Image:Protein file two0105.png (115 bytes)
    2: polar surface file of ectatomin
17. Image:File 1 6KLZ.pdb (0 bytes)
18. Image:File 8 6KM6al.pdb (0 bytes)
19. Image:File 8 6KM6.pdb (0 bytes)
20. Image:File 4 6KM2.pdb (0 bytes)

Page text matches

1. Help:Editing (24,612 bytes)
   55: : <nowiki><Structure load='Insert PDB code or filename here' size='X' frame='X' align='X' caption='I...
   57: ...er or an 'X' (and many of them are Optional). For example, this generates the Jmol structure applet on this...
   65: ====load='Insert PDB code or filename here' ====
   66: ...om Proteopedia's uploaded files. If your desired file is not in the PDB database and not yet uploaded t...
   114: '''<nowiki><Structure load='Insert PDB code or filename here' size='500' frame='true' align='right' c...
2. Scene authoring tools (23,035 bytes)
   6: ...ntent that includes these tags, but this page for example does not.
   11: Insert PDB code or filename here' size='350' frame='true' align='right' c...
   16: ...roteopedia's Scene Authoring Tools]] for tutorial examples.
   35: [[Image:Load_molecule.png|thumb|The load molecule tab in action]]
   38: ... first input area and click the load button. The file will be fetched from the PDB database.
3. FirstGlance in Jmol Literature Citations (31,234 bytes)
   17: ...9100 FirstGlance YouTube Channel] [[Image:Youtube.png]]
   69: [[Image:Sefid-consurf-teplizumab-2025.png]]
   78: [[Image:Garcia-e-lyta-fig5-microorgs2025.png|300px]]
   95: [[Image:Martinez-alcantar-2024-fig1-1ol5.png|500px]]
   119: ... et al 2024 Fig3C Isolated domain from AlphaFold2.png|400px]]
4. Image:Super-6xr8-6xra-theis-cao.pdb (217 bytes)
   1: See remarks in file:
   4: REMARK File name: Super-6xr8-6xra-theis-cao.pdb
   6: Original file by Eric Martz
5. User:Wayne Decatur/UNH BCHEM833 Structural Analysis Workshop Session Fall 2012 (17,130 bytes)
   23: ...7]], [[4aic]], [[2j3x]],[[3qmd]], or [[3pgx]] for examples. <small>Rare and when present are often unclear ...
   24: ...cialized sites and interfaces (just a few of many examples)
   30: ...ture Structure, Protein Science <nowiki>[</nowiki>example [http://onlinelibrary.wiley.com/doi/10.1002/pro.9...
   74: * [[Special:Upload]] List of allowed file types: png, jpg, jpeg, tiff, tif, gif, mgif, pdb, cif, mmcif...
   111: ***[http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=103 ''Compare'' Command Demonst...
6. Sandbox Reserved 703 (6,062 bytes)
   10: ...e where these lipids can be removed, reducing for example the amount of arterial cholesterol.
   46: ...b.org/pdb/explore/explore.do?structureId=2V3Q PDB file on 2v3q]
7. Emily Ellis/Sandbox (4,395 bytes)
   3: <qt>file=Image:salbutamol.mp4|autoplay=false|width=600|hei...
   14: ...s, such as the drug salbutamol we are using as an example here, are different from their mirror image. The ...
   71: [[Category:3D printer files]]
8. Sandbox UC 25 (4,096 bytes)
   3: ...exes can adopt certain conformations more likely. Examples are shown checking at the available data in the ...
   26: === Files not found ===
   28: ...s given by the NDB server did not have associated files. Particularly:
   32: ...However, the PDB ID does not exist inside the NDB files. The described structure corresponds to the Trp ...
   35: ...': Found in the NDB but with broken links. Proper files were downloaded from the PDB (PDB ID 2KAL).
9. User:Myriam Deshaies/Sandbox 1 (15,676 bytes)
   9: [[Image:2zet.png|left|200px]] {{STRUCTURE_2zet| PDB=2zet | SCEN...
   27: ...lls. It has several Rab27B effector proteins. For example, the interaction of Rab27B with Slac2-c/MyRIP is ...
   145: ...b.org/pdb/explore/explore.do?structureId=2ZET PDB file on 2ZET]
   146: ...b.org/pdb/explore/explore.do?structureId=2IEZ PDB file on 2IEZ]
   147: ...b.org/pdb/explore/explore.do?structureId=2F7S PDB file on 2F7S]
10. Missing residues and incomplete sidechains (25,887 bytes)
    11: ...issing in the atomic model. ({{font color|#c000c0|Example: 5 residues are missing from the carboxy terminus...
    18: ...sider [[Renumbering PDB files|renumbering the PDB file]].
    22: ...king them with spherical "empty baskets". In the example shown below, [[2ace]], the 3 missing N-terminal r...
    29: [[Image:2ace-fg-missing-nterm.png]]
    31: [[Image:2ace-pymol-missing-nterm.png|105px]]
11. User:Jaime Prilusky/Test/Jmol versions (1,239 bytes)
    21: ...d on SAT, simply loading the same file Fig1a_6b1l.png and saving.
    25: ...g_1a_sfx_labels_png/1'>from 008_Fig_1a_SFX_Labels.png without DORESIZE</scene>
    27: ...ame='10/1062580/Fig1a_6b1l_png/1'>from Fig1a_6b1l.png</scene>
12. Journal:Acta Cryst D:S2059798324005461 (10,979 bytes)
    13: ...g to their compartmentalization and expression profile. The prototypes of types I and II (in Class 1), a...
    16: ...enzyme<ref>PMID:8434007</ref> and may serve as an example of a <scene name='10/1050894/Ecaii_3eca/4'>Class ...
    19: ...e-refined in order to remove the shortcomings. An example can be seen in the high-resolution structure of E...
    32: load file "/cgi-bin/pprstr?bc356b44effd36197439439e31c1852b...
    39: load file "/cgi-bin/pprstr?bc356b44effd36197439439e31c1852b...
13. Image:Ejem.pdb (28 bytes)
    1: First model of 2KX5 pdb file
14. User:Eric Martz/Introduction to Structural Bioinformatics I (15,931 bytes)
    21: # Email your .pptx file to '''emartz@microbio.umass.edu''' for grading.--...
    37: Image:1000px-Amino Acids.svg.png|200 px|
    38: ...pedia.org/wiki/images/1/13/1000px-Amino_Acids.svg.png]
    64: ...s an ensemble of models consistent with the data. Examples: [[2bbn]]
    70: ... code called a '''PDB identification code''', for example
15. Tutorial:Basic Chemistry Topics (26,854 bytes)
    3: [[Image:1m4d.png|left|400px]]<ref name="Main Image">Vetting, M. W....
    7: ...epts are explained using a research article as an example. Applying general chemistry to a research article...
    53: .... Web. 26 Nov.2012. <http://en.wikipedia.org/wiki/File:Periodic_table.svg>. </ref>]]
    58: [[Image:Periodic Table (oxygen).png| thumb | center | 300px ]]
    99: [[Image:Amino Acid.png| thumb | left | 180px ]]
16. 1you (5,399 bytes)
    26: ...gned based on a lead inhibitor identified through file screening. Incorporation of a biaryl ether moiety...
17. Group:SMART:A Physical Model of the beta-Adrenergic Receptor (6,969 bytes)
    8: ...t on a member of the GPCR family of proteins. One example of a GPCR targeted by pharmaceutical companies is...
    10: ...MP, which induces a response within the cell (for example, muscle contraction if the receptor is located on...
    22: ...dinates for this structure as reported in the pdb file 2rh1, from the Ray Stevens laboratory at the Scri...
    40: A ply file describing this final structure was exported from...
18. 1r3i (4,720 bytes)
    24: ...ions diffuse across the cell membrane in a single file through the narrow selectivity filter of potassiu...
19. 1r3j (4,746 bytes)
    24: ...ions diffuse across the cell membrane in a single file through the narrow selectivity filter of potassiu...
20. 1r3k (4,693 bytes)
    24: ...ions diffuse across the cell membrane in a single file through the narrow selectivity filter of potassiu...

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