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1. 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...
2. User:Myriam Deshaies/Sandbox 1 (15,676 bytes)
   9: [[Image:2zet.png|left|200px]] {{STRUCTURE_2zet| PDB=2zet | SCEN...
   21: ... melanosome and then recruits melanophilin, which finally bounds myosin-Va. Because Rab27A and Rab27B are...
   83: ...T' size='500' frame='true' align='right' caption='Final model of 2zet: Two Rab27B/Slac2-a complexes (A/C ...
   89: The final model of 2ZET includes:
   145: ...b.org/pdb/explore/explore.do?structureId=2ZET PDB file on 2ZET]
3. Tutorial:Basic Chemistry Topics (26,854 bytes)
   3: [[Image:1m4d.png|left|400px]]<ref name="Main Image">Vetting, M. W....
   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 ]]
   198: [[Image:PH scale.png| thumb | center | 600px ]]
4. 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...
   38: --- Finally, <scene name='Hoelzer_Sandbox/Spacefilled_4/9'>...
   40: A ply file describing this final structure was exported from RP-RasMol and sent to...
5. Morphs (23,799 bytes)
   71: ...ript commands while displaying the same morph PDB file.
   75: ...r making true movies''' from multiple-model [[PDB files]], e.g. morphs, include:
   108: ...Empirical models|empirical]], [[atomic coordinate files]] that represent different conformations of the ...
   110: Before making a new morph from published PDB files, search the [http://molmovdb.org/cgi-bin/movie.c...
   114: ...s, and finally between the last key frame and the final empirical conformation. Examples of such morphs a...
6. Sandbox Reserved 706 (15,676 bytes)
   9: [[Image:2zet.png|left|200px]] {{STRUCTURE_2zet| PDB=2zet | SCEN...
   21: ... melanosome and then recruits melanophilin, which finally bounds myosin-Va. Because Rab27A and Rab27B are...
   83: ...T' size='500' frame='true' align='right' caption='Final model of 2zet: Two Rab27B/Slac2-a complexes (A/C ...
   89: The final model of 2ZET includes:
   145: ...b.org/pdb/explore/explore.do?structureId=2ZET PDB file on 2ZET]
7. User:Tom Gluick/glutamine synthetase (32,696 bytes)
   41: ...the options. This one allows you to load the PDB file).<br/>
   42: ...bination of four letters or numbers signifies the file containing the coordinates to describe a crystal ...
   81: ...nds tab. The contacts can be downloaded as a PDF file. The contacts of interest are those represented ...
   91: ...set representation.<br/>[[Image:active_site_still.png]]
   100: [[Image:Salt bridge.png]]
8. Hoelzer Sandbox (7,639 bytes)
   31: ...dinates for this structure as reported in the pdb file 2rh1, from the Ray Stevens laboratory at the Scri...
   43: --- Finally, <scene name='Hoelzer_Sandbox/Spacefilled_4/9'>...
   45: A ply file describing this final structure was exported from RP-RasMol and sent to...
9. Lac repressor morph methods (4,788 bytes)
   11: ...he vicinity of those in 1L1M. The final morph PDB file is available within Proteopedia as [[Image:1osl_1...
   15: ...ols). (Some of the hydrogen atom names in the PDB file generated by Model It were misaligned so that [[S...
   20: ...h DOS program striph.exe). The resulting 12-model file was 1.6 megabytes, and was gzipped to 0.4 megabyt...
10. Sandbox Eric Martz (6,386 bytes)
    99: ...0-7. In the product morph, the orientation of the final chains was not changed. Hence, chain A (NEDD8) fr...
    123: ...ttp://www.ebi.ac.uk/msd-srv/pqs/pqs-bin/macmol.pl?filename=3DQV PQS]) with the Yale Morph Server (beta v...
11. User:Max Lein/Sandbox (6,051 bytes)
    1: [[Image:1gpa.png|left|200px]]
    5: ... may change the PDB parameter (which sets the PDB file loaded into the applet)
    27: ...The subunits make interactions that stabilize the final structure.
    36: ...o Ser14 near the N-terminus. This represents the final step in a signal transduction cascade in response...
12. Image:Final.pdb (397 bytes)
    1: ...ne the frames together into a single pdb). Source files are 1atu and 1ezx.
    3: ... Final.pdb isn't a great choice for a distinctive filename. Feel free to delete this if it gets in the ...
13. Sandbox99999 (4,644 bytes)
    24: ...dinates for this structure as reported in the pdb file 2rh1, from the Ray Stevens laboratory at the Scri...
    36: --- Finally, <scene name='Hoelzer_Sandbox/Spacefilled_4/9'>...
    38: A ply file describing this final structure was exported from RP-RasMol and sent to...
14. User:David Stack/Workbench (5,945 bytes)
    28: ...dinates for this structure as reported in the pdb file 1yjp, from the Howard Hughes Medical Institute, U...
    30: ...tack/Workbench/Prion_step_one/1'>the raw 1yjp pdb file</scene>, the format was set to ball and stick and...
    32: A ply file describing this final structure was exported from RP-RasMol and sent to...
15. Group:SMART:A Physical Model of the Structure of GNNQQNY from Yeast Prion Sup35 (5,995 bytes)
    26: ...dinates for this structure as reported in the pdb file 1yjp, from the Howard Hughes Medical Institute, U...
    28: ...tack/Workbench/Prion_step_one/1'>the raw 1yjp pdb file</scene>, the format was set to ball and stick and...
    30: A ply file describing this final structure was exported from RP-RasMol and sent to...
16. User:Danielle Ferguson/Workbench (6,625 bytes)
    34: ...dinates for this structure as reported in the pdb file 2I2T, from the _____laboratory at ____Research In...
    47: --- Finally, <scene name='Hoelzer_Sandbox/Spacefilled_4/8'>...
    49: A ply file describing this final structure was exported from RP-RasMol and sent to...
17. Electron density maps (12,314 bytes)
    1: [[Image:jmol_edm_tyr_1.0s.png|frame|Snapshot of 1.0 &Aring; electron density ma...
    22: ... correspondence between the published model [[PDB file]] and the electron density map (EDM) provides muc...
    33: [[PDB files]], e.g.
    37: [[Image:Edm-6zx4.png|right|275px]]
    38: [[Image:Edm-3u7z.png|right|225px]]
18. ConSurf Quick Analysis Procedure (2,841 bytes)
    7: ...de]] (or upload your [[Atomic coordinate file|PDB file]]) and click the ''Next'' button.
    19: ...op of the '''Job Status Page''', scroll down to ''Final Results'' and click ''View ConSurf Results with F...
    28: ....org FirstGlance.Jmol.Org], upload the downloaded file.
    30: * '''Right''' click the link ''PDB File with ConSurf Results in its Header, for FirstGlan...
19. Jasper Sandbox (4,458 bytes)
    5: ... may change the PDB parameter (which sets the PDB file loaded into the applet)
    23: ...tron density. The structure has been refined to a final R-factor of 19.8% for all data between 6 A and 1....
20. Jasper Final Sandbox (4,458 bytes)
    5: ... may change the PDB parameter (which sets the PDB file loaded into the applet)
    23: ...tron density. The structure has been refined to a final R-factor of 19.8% for all data between 6 A and 1....

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