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- Getting Unremediated PDB Files (5,391 bytes)
1: ...n order to better standardize and enhance the PDB files deposited before December 2, 2008. The details of...
11: ...e were repaired by obtaining the unremediated PDB files and using them for these scenes.)
14: ... 2007 remediation is that when the remediated PDB files contain DNA, [[Chime]]-based [[Protein Explorer]]...
17: ...ite] to easily get July 31, 2007 unremediated pdb files [ftp://snapshots.wwpdb.org/ via ftp at the RCSB P...
22: ... The 2007 files are .Z compressed, while the 2009 files are .gz compressed. - User:Wayne Decatur/Editing Getting Unremediated PDB Files (1,988 bytes)
1: All files obtained from the World Wide Protein Data Bank si...
9: ...ediated PDB files is that when the remediated PDB files contain DNA, Protein Explorer (and perhaps some o...
13: ...artz's UMASS site] to easily get unremediated pdb files [ftp://ftp.rcsb.org via ftp at the RCSB Protein D...
14: These files come back in a compressed form. Eric Martz's site... - Renumbering PDB files (4,010 bytes)
1: ... (residues) in [[atomic coordinate files]] ([[PDB files]]) are numbered. For polymers (protein, DNA, RNA)...
5: ...are servers that will re-number atomic coordinate files.
8: ...dinate file|mmCIF file format]] atomic coordinate files. PDBrenum does NOT process arbitrary models, such...
10: ... (HEC) in different orders in the text of the PDB files, so their numbers still don't match.
15: ... a server that has many options for modifying PDB files. The complete list of operations is explained in ... - Category:3D printer files (37 bytes)
1: Pages with files ready for 3D printer
Page text matches
- Help:Editing (24,612 bytes)
66: ... applet load the file from Proteopedia's uploaded files. If your desired file is not in the PDB database... - Hemoglobin (19,234 bytes)
57: ...form; and finally a summary overview. (from PDB files bio3HHB and bio1HCO) - 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 "aver... - User:Ignacio Ibarra Del Río/Workbench/Structural analysis of DNA structures (4,313 bytes)
29: === Files not found ===
31: ...s given by the NDB server did not have associated files. Particularly:
35: ...However, the PDB ID does not exist inside the NDB files. The described structure corresponds to the Trp o...
38: ...': Found in the NDB but with broken links. Proper files were downloaded from the PDB (PDB ID 2KAL).
42: ...sterior analysis showed modified bases in several files. The reported set was checked and structures were... - Molecular Playground/CheA (4,072 bytes)
12: ...le to date do not have all five domains. The PDB files included in this proteopedia page are <u><scene n... - 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 o...
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 were... - Missing residues and incomplete sidechains (25,887 bytes)
18: ...rot numbering. If not, consider [[Renumbering PDB files|renumbering the PDB file]].
312: ...Missing residues and atoms lists in PDB and mmCIF files==
314: Quoting from the legacy [https://files.wwpdb.org/pub/pdb/doc/format_descriptions/Format_...
328: ...ook for REMARK 465 and REMARK 470 in the [https://files.rcsb.org/view/2ACE.pdb PDB file for 2ACE].
350: Examination of mmCIF files suggests that missing residues are also indicated... - Engineered Protein Inhibitors of SARS-CoV-2 Entry (10,254 bytes)
58: ===PDB Files=== - New Test (8,065 bytes)
79: ===PDB Files=== - Sandbox Reserved 718 (9,261 bytes)
32: Protein Data Bank files [http://www.rcsb.org/pdb/explore/explore.do?struc... - Engineered Protein Inhibitors for SARS-CoV-2 Entry (8,053 bytes)
79: ===PDB Files=== - User:Matthew Pereira/Sandbox Experimental (5,791 bytes)
76: ===PDB Files=== - 1pxq (5,257 bytes)
14: ...ure calculations, starting with the same NMR peak files and assignments. The stereoisomer with the l ster... - User:Elizabeth Yowell/ SandboxFinal (5,599 bytes)
102: ===PDB Files=== - User:David Bogle/Sandbox 2 (3,116 bytes)
43: ====PDB Files====
44: PDB Files - User:Elizabeth Yowell/SandboxGiavanna (2,341 bytes)
38: ===PDB Files=== - Image:Test 4wto 1 PNGJ.png (46 bytes)
1: test for loading pre-made scenes as PNGJ files - Arsenite resistance protein (4,318 bytes)
8: The PDB files for ARS2 are given below. As can be seen, ARS2 bi... - User:Ignacio Ibarra Del Río/Workbench/Comparative modelling testing (1,770 bytes)
3: === Preparing the modelling structure files ===
15: ...plate-target pairs were generated in terms of PIR files (note: a sequence can be matched with a template ... - How to see conserved regions (2,898 bytes)
25: ...face to FirstGlance removed in 2022, so these PDB files no longer work in FirstGlance.
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