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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. Image:FILE consurf1243922409 pipe.pdb (0 bytes)
4. Image:FILE consurf1240241051 pipe.pdb (0 bytes)
5. Image:FILE consurf1240240806 pipe.pdb (0 bytes)
6. Image:FILE consurf1254065510 pipe.pdb (33 bytes)
7. 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...
8. Image:Pdb file diagram.png (0 bytes)
9. 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.
10. Image:Upload file.png (0 bytes)
11. Image:ASGR1 homology model PDB file.pdb (85 bytes)
12. Image:ASGR1 homology model PDB file.pdb.gz (85 bytes)
13. Image:Protein file two0105.png (115 bytes)
    2: polar surface file of ectatomin
14. Image:File 1 6KLZ.pdb (0 bytes)
15. Image:File 8 6KM6al.pdb (0 bytes)
16. Image:File 8 6KM6.pdb (0 bytes)
17. Image:File 4 6KM2.pdb (0 bytes)
18. Jmol/PDB file editing with Jmol (8,487 bytes)
    1: ... [[Jmol#Command_Scripting_Language|command script file]] can be written to make specific changes, follow...
    6: Before you make any edited PDB file public, such as by uploading it to Proteopedia, P...
    8: ===Use a distinctive PDB file name===
    10: Do not give your PDB file a name that is easily confused with the version p...
    12: ==Put the PDB file in a variable==
19. Header of PDB file (3,217 bytes)
    1: [[PDB files]] contain atomic coordinates plus additional ann...
    36: ...e HEADER record, which is the first line in a PDB file, and always a single line. Here is the HEADER rec...
    43: ...be/static/entry/1hxw.header Header section of PDB file 1hxw].
    44: ...ebi.ac.uk/pdbe/entry-files/pdb1hxw.ent Entire PDB file 1hxw]. Following the header section are the ATOM ...
    49: ...lick ''Show More Details'', then click ''View PDB File''.
20. Image:ASGR1 homology model PDB file Edited.zip (27 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...
   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)
   11: Insert PDB code or filename here' size='350' frame='true' align='right' c...
   38: ... first input area and click the load button. The file will be fetched from the PDB database.
   40: ...area next to the words "From Proteopedia uploaded file" and click load.
   42: ..."load" command. For example, you can load a .PNGJ file to load coordinates and a 3D scene in one step.
   48: ...page, search for <code style="color:maroon">load "filename" FILTER</code>).
3. FirstGlance in Jmol Literature Citations (30,325 bytes)
   219: ...e grade as defined by FirstGlance in Jmol .... '''Files were kept if their Rfree grade was at least "ave...
   224: ...ttila ''et al.'' 2020 provided a downloadable PDB file with a link to view it by uploading to ''FirstGla...
   229: ...ttp://op.niscpr.res.in/index.php/IJBB/article/viewFile/29116/465477657 Zaheer ZA, Sankaranarayanan K. In...
   275: * [https://www.researchgate.net/profile/Rahul-Shelake/publication/309241483_Structural_An...
   317: ...l'' that will allow the reader to call up the pdb file in a simple Web-based viewer that is browser inde...
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)
   74: * [[Special:Upload]] List of allowed file types: png, jpg, jpeg, tiff, tif, gif, mgif, pdb,...
6. Sandbox Reserved 703 (6,062 bytes)
   46: ...b.org/pdb/explore/explore.do?structureId=2V3Q PDB file on 2v3q]
7. Emily Ellis/Sandbox (4,365 bytes)
   3: <qt>file=Image:salbutamol.mp4|autoplay=false|width=600|hei...
8. Sandbox UC 25 (4,096 bytes)
   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).
   39: ...sterior analysis showed modified bases in several files. The reported set was checked and structures wer...
9. User:Myriam Deshaies/Sandbox 1 (15,676 bytes)
   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]
   148: ...b.org/pdb/explore/explore.do?structureId=2IEY PDB file on 2IEY]
   149: ...b.org/pdb/explore/explore.do?structureId=2IFO PDB file on 2IFO]
10. Missing residues and incomplete sidechains (25,887 bytes)
    18: ...sider [[Renumbering PDB files|renumbering the PDB file]].
    96: ...download the AlphaFold model]. The downloaded PDB file can then be uploaded to [http://firstglance.jmol....
    295: ...ill in incomplete sidechains in [[2ace]], the PDB file was loaded into [[Swiss-PDBViewer]], then saved. ...
    304: ...ich also lists all the missing residues (from PDB file REMARK 465).
    312: ...Missing residues and atoms lists in PDB and mmCIF files==
11. User:Jaime Prilusky/Test/Jmol versions (1,239 bytes)
    21: ...wo scenes created on SAT, simply loading the same file Fig1a_6b1l.png and saving.
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...
    32: load file "/cgi-bin/pprstr?bc356b44effd36197439439e31c1852b...
    39: load file "/cgi-bin/pprstr?bc356b44effd36197439439e31c1852b...
    47: load file "/cgi-bin/pprstr?bc356b44effd36197439439e31c1852b...
    55: 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.--...
    121: Save your report with the filename '''yourLastName-565.pptx''', for example <fon...
    129: ...oint Assignment] (You may download it, rename the file, and use it as a template.)
    195: #Drag the image file (filename ending in .gif) from the Desktop and drop it ...
    196: ..., the animation will run only when the saved .ppt file is projected (full screen).
15. Tutorial:Basic Chemistry Topics (26,854 bytes)
    53: .... Web. 26 Nov.2012. <http://en.wikipedia.org/wiki/File:Periodic_table.svg>. </ref>]]
    233: .... Web. 31 Oct. 2012.<http://en.wikipedia.org/wiki/File:NaF.gif.</ref>]]
    240: .... 31 Oct. 2012 <http://commons.wikimedia.org/wiki/File:3D_model_hydrogen_bonds_in_water.jpg.</ref>]]
    293: ...rce used by the body.<ref>Maňas, Michal, trans. "File:3D model hydrogen bonds in water.jpg." "Coenzyme ...
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)
    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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