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  1. Image:Morph-lin-6vr4-to-af2-CAO.pdb (0 bytes)
  2. Image:Morph-lin-6vr4-to-2nd-CAO.pdb (0 bytes)
  3. Image:1QLNA 1MSWD 10.morph.pdb (68 bytes)
    1: ...terpolating between structure 1QLNA.pdb and 1MSWD.pdb
  4. Image:Canner HIV morph.pdb (0 bytes)
  5. Image:1a0r-vs-af3-morph-licorice-far.gif (0 bytes)
  6. Image:1yve i knot morph.pdb (155 bytes)
  7. Image:1tph 1 noknot morph.pdb (43 bytes)
  8. Image:Pasted morph.pdb (0 bytes)
  9. Image:1osl 19 1l1m 9 morph.pdb (280 bytes)
  10. Lac repressor morph methods (4,788 bytes)
    11: ...ithin Proteopedia as [[Image:1osl_19_1l1m_9_morph.pdb]].
    15: ...rated by Model It were misaligned so that [[Swiss-PDBViewer_%3D_DeepView|DeepView]] did not include the...
    20: ...ne with the [http://www.umass.edu/microbio/rasmol/pdbtools.htm freely available DOS program morph2.exe]...
  11. Image:1osl 14 1l1m 9 morph.pdb (225 bytes)
    1: ...uplicate of the file [[Image:1osl_19_1l1m_9_morph.pdb]] because I had problems loading that file.
  12. User:Wayne Decatur/I-Ppo Morph Methods (7,548 bytes)
    1: ....org molvisindex.org] under Molecules, Sources of PDB Files, under DNA Tools) as described in [[Lac rep...
    2: ...ng server].<nowiki>]</nowiki> Editing text of the pdb file, I deleted the 'A' at the three prime end of...
    4: ...erated by Model IT), I needed to get unremediated pdb file for 1a73 or completely alter the order of th...
    6: ...3 structure into [http://spdbv.vital-it.ch/ Swiss-pdb viewer (DEEP VIEW)] and let it magic fit the apo ...
    9: ...es_using_BioPython the help site for manipulating pdb files with Biopython] and also the [http://biopyt...
  13. Image:3dpl 3dqv acr morph.pdb (632 bytes)
    2: ...was not changed. Hence, chain A (Nedd8) from 3dqv.pdb was added as model number 8 (9th model) without t...
  14. Image:Morph 2ipy-2b3x.pdb.gz (96 bytes)
  15. Image:3dqv trimer1 trimer2 morph.pdb.gz (153 bytes)
  16. Image:2oau 2vv5 morph.pdb.gz (93 bytes)
  17. Image:2oau 2vv5 morph cao.pdb.gz (228 bytes)
  18. Image:2oau 2vv5 27-112 morph.pdb.gz (284 bytes)
    2: ...a.cgi) of 2oau to 2vv5. Prior to submitting these PDB files, residues 113-281 were deleted, leaving onl...
  19. Image:B-Z Morph Movie.mpg (55 bytes)
  20. Image:Morph a-b.pdb (29 bytes)

Page text matches

  1. User:Karsten Theis/Rigid body interpolation (4,709 bytes)
    114: // fname = "morph" + i + ".pdb"
  2. Image:3hg2to3.pdb.gz (19 bytes)
  3. Image:Better3hg2to3.pdb.gz (18 bytes)
  4. Art:Spike protein conformation change (371 bytes)
  5. Teaching Scenes, Tutorials, and Educators' Pages (12,171 bytes)
    144: ...e [[:Category:RCSB_PDB_Molecule_of_the_Month|RCSB PDB Molecule of the Month]].
    155: <td>[http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_06 Vaults]</td>
    160: <td>[http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_05 Influenza Neuraminidase]</td>
    165: <td>[http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_04 Oct and Sox Transcription Factors]</t...
    170: <td>[http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_03 Hydrogenase]</td>
  6. Missing residues and incomplete sidechains (25,887 bytes)
    6: ...RCSB].</ref> of the [[Empirical models]] in the [[PDB]], some residues (amino acids or nucleotides) tha...
    18: ... consider [[Renumbering PDB files|renumbering the PDB file]].
    96: ....uk download the AlphaFold model]. The downloaded PDB file can then be uploaded to [http://firstglance....
    209: ...ame="oca" /> of the [[Empirical models]] in the [[PDB]], some residues have coordinates missing for som...
    295: ...in [[2ace]], the PDB file was loaded into [[Swiss-PDBViewer]], then saved. It completes sidechains auto...
  7. User:Alexander Grayzel/Sandbox 1 (15,974 bytes)
  8. Sculpting protein conformations (6,480 bytes)
  9. Sandbox UC 9 (2,556 bytes)
    1: <Structure load='Insert PDB code or filename here' size='350' frame='true' al...
    21: ...-model PDB file is [[Image:Morph-linear-1trh-1lpm.pdb.gz]].</ref> shows the lid opening and closing.
  10. Proteopedia:Practical Guide to Advanced Proteopedia Authoring and Its Use in Teaching (16,838 bytes)
  11. Image:3hg3to4.pdb.gz (87 bytes)
  12. AlphaFold2 examples from CASP 14 (26,979 bytes)
    20: ...ell</scene><ref name="imf">Superposition by Swiss-PdbViewer's ''iterative magic fit''. This starts with...
    23: ...alpha carbons<ref name="fitselimprov">Using Swiss-PdbViewer's ''Fit from Selection'' with 102 residues ...
    27: ..._PDB/T1064-D1/T1064TS427_1-D1.pdb T1064TS427_1-D1.pdb].</ref> has a '''GDT_TS score of 87'''. (A score ...
    48: ... Server]] by linear interpolation.</ref> of Swiss-PdbViewer 4.1.<br>
    49: ... "Iterative Magic Fit"<ref name="imf" /> of Swiss-PdbViewer 4.1.'''<br>
  13. User:Eric Martz (29,690 bytes)
    15: PDBRedo (on Quality & Retractions)
    133: ===Molecules: PDB Code-Titled Pages===
    135: ...cation, they speculated that it was a trimer. The PDB file deems it a monomer.
    189: **[[Converting AlphaFold3 CIF to PDB]]
    200: *[[Atomic coordinate file]] <- [[PDB file]], [[PDB file format]]
  14. Eric Martz's Favorites (2,342 bytes)
    17: ...over a dozen other categories containing over 150 PDB entries. Each structure is liked for further expl...
  15. Proteopedia:Wishlist (29,517 bytes)
    14: ** Incorporate a remark into PDB when copying an uploaded file to getfrozenstructu...
    15: ** Incorporate a remark into PDB when returning a morph from the pymol morph serve...
    16: ...ncorporate source information and their name into PDB headers before they upload
    38: ...list, already linked, were at the bottom of every PDB-code-titled page. OCA already does sequence-based...
    49: ...' of PDB codes on Category pages (in this order): PDB code, resolution, year, title, authors (ideally f...
  16. Proteopedia:Topic Pages (8,541 bytes)
    1: ...rchy of page organization in Proteopedia than are PDB-code-titled pages. The list of structures relate...
    7: ==Pages About Molecules (Not Titled with a PDB Code)==
    9: ...r families of molecules that are not named with a PDB code, and that also have substantial content. Bec...
    160: ==PDB Code Pages==
    161: ...s a manually maintained list of pages titled with PDB codes that have especially well-developed content...
  17. Synthetic nanomaterials from standardized protein blocks (12,946 bytes)
    25: ...he following assemblies that can be downloaded as PDB files from supplementary materials of Huddy ''et ...
    28: ...ude<ref>The assemblies shown can be downloaded as PDB files from supplementary materials of Huddy ''et ...
    79: ... /wiki/images/0/0b/Huddy-cage-o4-32-assembly-morf.pdb.gz;
    97: ==PDB Files==
    98: ...et al.'', 2024<ref name="huddy2024" />, or below. PDB files obtained from Huddy ''et al.'', 2024 or der...
  18. Proteopedia:Problems (18,636 bytes)
    9: ...010 (IST) This is a related problem to the latest PDB file remediation. Solved for these structures but...
    36: ...uary 2009 (IST) ♣ This is not really a problem. PDB (RCSB) is not required to name ligands and short ...
    40: ...'SOLVED'''</span> '''PDB code case:''' Lower case PDB codes work in internal links, e.g. [[4cpa]], but ...
    43: ...sed '''before''' finally applying a category to a PDB. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 F...
    45: ...le buttons fail. An example is [[2zkr]], the only PDB entry with 62 chains (in January 2011). Also in s...
  19. Proton Channels (2,108 bytes)
  20. Image:Tres EH eMorph.pdb (57 bytes)

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