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- 06:08, 3 January 2010 Wayne Decatur (Talk | contribs) uploaded "Image:2j01and2j00andrestofAsitetRNAalphac.pdb.gz" (pdbs 2j01 and 2j00 and rest of A-site tRNA from 1jgo ALL run through alphac with tRNA atoms added back)
- 03:46, 3 January 2010 Wayne Decatur (Talk | contribs) uploaded "Image:Par.png" (made with older version of jmol not in Proteopedia so didn't fix quality REMAKE WITH PROTEOPEDIA ONE SOON)
- 03:16, 3 January 2010 Wayne Decatur (Talk | contribs) uploaded a new version of "Image:Azithromycin50s.png"
- 02:50, 3 January 2010 Wayne Decatur (Talk | contribs) uploaded "Image:Azithromycin50s.png" (made with page in Proteopedia)
- 07:42, 31 December 2009 Wayne Decatur (Talk | contribs) uploaded a new version of "Image:Azithromycin50s.jpg" (fixed edges so no border showing)
- 07:39, 31 December 2009 Wayne Decatur (Talk | contribs) uploaded "Image:Azithromycin50s.jpg" (Azithromycin bound to Haloarcula 50S made with page in proteopedia that I made)
- 07:05, 31 December 2009 Wayne Decatur (Talk | contribs) uploaded "Image:1m1kalphac.pdb.gz" (gzipped 1m1k with with Erix Martz's alphac run and then the water stripped out and the original connect files added back)
- 06:33, 31 December 2009 Wayne Decatur (Talk | contribs) uploaded a new version of "Image:Azithromycin.pdb" (gzipped version now)
- 05:39, 31 December 2009 Wayne Decatur (Talk | contribs) uploaded "Image:Azithromycin.pdb" (Azithromycin extracted from pdb file 1m1k)
- 05:01, 18 December 2009 Wayne Decatur (Talk | contribs) uploaded "Image:2j01and2j00andrestofAsitetRNABACKBONE.pdb.gz" (2j01 and 2j00 with NOTE: This particular model has been modified to have nts 1-25 and 45-76 of the A-site tRNA added back on from 1gix (= tRNAs in 1jgo) files by hand-fitting of those tRNAs on that of those in 2j00. Model 3 (chain b) is this part of the )
- 05:01, 7 December 2009 Wayne Decatur (Talk | contribs) uploaded a new version of "Image:1s72ALPHACplusccapurowithCERTAINSIDECHAINS.PDB" (I mistakenly left an atom with wrong chain designation and this fixed!)
- 04:27, 7 December 2009 Wayne Decatur (Talk | contribs) uploaded a new version of "Image:1s72ALPHACplusccapurowithCERTAINSIDECHAINS.PDB" (started with 1s72ALPHACplusccapuro.PDB and now I added certain amino acids close to the critical atom of Yarus analog as well as 2 nts that base pair with the analog and nt 2486. Derived from 1s72 with CCA-puromyxin from 1ffz )
- 02:19, 7 December 2009 Wayne Decatur (Talk | contribs) uploaded a new version of "Image:1s72ALPHACplusccapurowithCERTAINSIDECHAINS.PDB" (started with 1s72ALPHACplusccapuro.PDB and now I added certain amino acids close to the critical atom of Yarus analog as well as 2 nts that base pair with the analog. Derived from 1s72 with CCA-puromyxin from 1ffz )
- 02:14, 7 December 2009 Wayne Decatur (Talk | contribs) uploaded "Image:1s72ALPHACplusccapurowithCERTAINSIDECHAINS.PDB" (started with 1s72ALPHACplusccapuro.PDB and now I added certain amino acids close to the critical atom of Yarus analog as well as 2 nts that base pair with the analog. Derived from 1s72 with CCA-puromyxin from 1ffz)
- 05:12, 6 December 2009 Wayne Decatur (Talk | contribs) uploaded "Image:Withheader1s72ALPHACplusccapuro.PDB" (derived from pdb file To test whether HELIX and SHEET info adds anything from what I saw with 1s72ALPHACplusccapuro.PDB.gz where I didn't add the header back)
- 21:10, 29 November 2009 Wayne Decatur (Talk | contribs) uploaded a new version of "Image:Schematic hmarlsu.jpg" (schematic of Haloarcula marismortui 23S rRNA)
- 20:52, 29 November 2009 Wayne Decatur (Talk | contribs) uploaded "Image:Schematic hmarlsu.jpg" (schematic of Haloarcula marismortui 23S rRNA)
- 07:20, 29 November 2009 Wayne Decatur (Talk | contribs) uploaded a new version of "Image:Dna three way junction sequence.jpg" (DNA sequence in the structure)
- 03:04, 29 November 2009 Wayne Decatur (Talk | contribs) uploaded "Image:Dna three way junction sequence.jpg" (DNA sequence in the structure)
- 03:50, 28 November 2009 Wayne Decatur (Talk | contribs) uploaded "Image:1gm5 showing chains ADP.png" (Made with Jmol)
- 02:50, 28 November 2009 Wayne Decatur (Talk | contribs) uploaded "Image:1gm5 showing chains.png" (made using Jmol)
- 05:41, 2 November 2009 Wayne Decatur (Talk | contribs) uploaded "Image:1s72ALPHACplusccapuro.PDB.gz" (1s72 where nucleic and proteins just phosphorus and alpha carbon backbone but where i added back CCA-puro from 1ffz as chain 5)
- 02:27, 2 November 2009 Wayne Decatur (Talk | contribs) uploaded "Image:1s72simplified.PDB.gz" (Ran Eric Martz's alphac 2.0 on 1s72 to simplify)
- 01:38, 2 November 2009 Wayne Decatur (Talk | contribs) uploaded "Image:Lsu side and front white background.png" (1s72 from side and front using Swiss PDB viewer)
- 20:21, 1 November 2009 Wayne Decatur (Talk | contribs) uploaded a new version of "Image:3ews3g0hJUSTSTARTEND.pdb" (3ews and 3g0h in a single file as they had been morphed by Yale Server. The intermediate models were removed and the extra atoms for 3ews added back in by Magicfit in Swiss PDB viewer. )
- 20:21, 1 November 2009 Wayne Decatur (Talk | contribs) uploaded a new version of "Image:3ews3g0hJUSTSTARTEND.pdb" (3ews and 3g0h in a single file as they had been morphed by Yale Server. The intermediate models were removed and the extra atoms for 3ews added back in by Magicfit in Swiss PDB viewer. )
- 20:20, 1 November 2009 Wayne Decatur (Talk | contribs) uploaded "Image:3ews3g0hJUSTSTARTEND.pdb" (3ews and 3g0h in a single file as they had been morphed by Yale Server. The intermediate models were removed and the extra atoms for 3ews added back in by Magicfit in Swiss PDB viewer. )
- 04:22, 1 November 2009 Wayne Decatur (Talk | contribs) uploaded "Image:3g0hSIMPLER.jpg" (The default image Image:3g0h.png looked quite complex so I made a simpler one still in the style of many of the default images.)
- 01:21, 1 November 2009 Wayne Decatur (Talk | contribs) uploaded "Image:3ewsBIOLUNIT1.pdb.gz" (Biological unit 1 since asymmetric unit has 2)
- 23:13, 31 October 2009 Wayne Decatur (Talk | contribs) uploaded "Image:3ews3g0hmorphBETTER.pdb.gz" (Morph of 3ews to 3g0h. Improved by adding back the ligands and RNA and the extra atoms to model 1 that came from using magicFit to translate it over automatically in Swiss-PDB Viewer)
- 04:49, 31 October 2009 Wayne Decatur (Talk | contribs) uploaded "Image:3ews3g0hmorphFIXED.pdb.gz" (See Image:3ews3g0hmorph.pdb.gz because I don't feel like entering all the information again since I had to spend time fixing this and don't know if it is done yet.)
- 04:31, 31 October 2009 Wayne Decatur (Talk | contribs) uploaded "Image:3ews3g0hmorph.pdb.gz" (morph of 3ews to 3g0h gzipped No copyright since PDB says pdb files and derived files aren't protected.)
- 03:01, 23 October 2009 Wayne Decatur (Talk | contribs) uploaded "Image:3fpntorotatedversion.pdb" (3fpn normal view morphed to view like in Figure 3 of paper describing structure. There is no copyright as PDB says no copyright on PDB files or files derived from them.)
- 20:24, 18 October 2009 Wayne Decatur (Talk | contribs) uploaded "Image:2eyqBIOLUNIT.pdb" (Biological Unit of 2eyq. No copyright needed since the PDB says PDB files and those derived do not fall under copyrights.)
- 20:25, 8 October 2009 Wayne Decatur (Talk | contribs) uploaded "Image:SSU front and LSU front side by side white backgroundSMALL.jpg" (SSU from Ramakrishnan work with A-site Anticodon Stem Loop bound as well as mRNA analaog show. LSU from Steitz and Moore labs work shown. Derived from PDB files available at Protein Data Bank which says they have no copyright if you use derived structur)
- 20:05, 8 October 2009 Wayne Decatur (Talk | contribs) uploaded "Image:Screen capture of 70S white background spacefill tRNAS.jpg" (screen capture (most anything else causes crash) of 70S ribosome from Pymol. This is the Noller 2.8 Angstrom structure (2j00 and 2j01) with the A-site tRNA from the 5.5 Angstrom (1gix) fit back in with the portion seen at 2.8 Angstrom. According to Prote)
- 00:59, 2 October 2009 Wayne Decatur (Talk | contribs) uploaded "Image:3dmqBIOLUNIT.pdb" (biological molecule 1 of 3dmq from http://www.pdb.org/pdb/explore/explore.do?structureId=3DMQ From the PDB "Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both )
- 05:39, 27 September 2009 Wayne Decatur (Talk | contribs) uploaded "Image:2db3BIOMOL.pdb" (biological molecule 1 of 2db3 from http://www.rcsb.org/pdb/explore/explore.do?structureId=2DB3 From the PDB "Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both)
- 04:47, 27 September 2009 Wayne Decatur (Talk | contribs) uploaded "Image:1r9fTRUBIOUNIT.pdb" (biological unit of 1r9f from http://www.rcsb.org/pdb/files/1R9F.pdb1.gz (REMOVED THE MODEL NUMBERS AND SECOND RNA and made second A chain D using a python script (SEE BELOW) From the PDB "Data files contained in the PDB archive (ftp://ftp.wwpdb.org) ar)
- 04:28, 27 September 2009 Wayne Decatur (Talk | contribs) uploaded "Image:1r9fTRUEBIOLUNIT.pdb" (biological unit of 1r9f from http://www.rcsb.org/pdb/files/1R9F.pdb1.gz From the PDB "Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and co)
- 04:12, 27 September 2009 Wayne Decatur (Talk | contribs) uploaded "Image:1r9f biolunit.pdb" (biological unit of 1r9f from http://www.rcsb.org/pdb/files/1R9F.pdb1.gz)
- 03:05, 20 April 2009 Wayne Decatur (Talk | contribs) uploaded "Image:1l8bmonomer.pdb" (Just one monomer of the Messenger RNA 5' Cap-binding Protein (eIF4E) bound to 7-methylGpppG. The original file 1l8b had two in the unit cell of the crystal structure, in contrast to the biological unit. From the PDB "Data files contained in the PDB archi)
- 05:55, 1 February 2009 Wayne Decatur (Talk | contribs) uploaded "Image:2az0WithPolyview3D.png" (2az0 with Polyview-3D Settings used: Data source: PDB code=2az0 Initial rotation around X axis: -85.5 Initial rotation around Y axis: -77.2 Initial rotation around Z axis: 38.1 Rendering program: PyMol Type of image: Static slide Background color Red fac)
- 22:48, 29 January 2009 Wayne Decatur (Talk | contribs) uploaded "Image:1jgo1giy.gz.pdb" (pdb files 1jgo and 1giy as one gzipped file for use with jmol See Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, and Noller HF. 2001. Crystal structure of the ribosome at 5.5 Å resolution. Science 292:883-896. Epub 2001 Mar 29. an)
- 21:41, 27 November 2008 Wayne Decatur (Talk | contribs) uploaded "Image:2h9cmorph2h9d.pdb" (morph of 2h9c to 2h9d a and b chains. Pyruvate of 2h9d model added back by magic fitting 2h9d to last model of morph and extracting the 204 and 205 set of pyr atoms.)
- 07:04, 27 November 2008 Wayne Decatur (Talk | contribs) uploaded "Image:2h9dmorph8.pdb" (8 model morph of chains A and B of 2h9d to chains C and D of 2h9d with pyruvates placed using magic fit of A and B part to first model and C and D part to last model.)
- 23:13, 25 November 2008 Wayne Decatur (Talk | contribs) uploaded "Image:1atu1ezxwd.pdb" (Daniel Seeman's file with just model numbers fixed by find and replace)
- 22:54, 25 November 2008 Wayne Decatur (Talk | contribs) uploaded "Image:1atu 1ezxwd30.pdb" (models 1-30 of Daniel Seeman's morph)
- 21:01, 25 November 2008 Wayne Decatur (Talk | contribs) uploaded "Image:Dsmorph.pdb" (Models 1-6 of Daniel Seeman's morph)
- 20:57, 25 November 2008 Wayne Decatur (Talk | contribs) uploaded "Image:Ds models1-6.pdb" (Models 1-6 of Daniel Seeman's morph)
