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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)
    1: Morph of pulling a knot in [[1yve]] chain I. Data kindl...
  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)
    1: ... construct this morph, please see [[Lac_repressor_morph_methods]].
  10. Lac repressor morph methods (4,788 bytes)
    1: ...his page describes the methods used to create the morph displayed at:
    3: * [[Lac repressor#Morph of Conversion]]
    4: * [[Morphs]]
    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...
  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: ... under DNA Tools) as described in [[Lac repressor morph methods]]. <nowiki>[</nowiki>UPDATE: The Model It...
    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 ...
    8: ...o that I could match up the number of atoms since morphing needs equal numbers. I also needed to change ...
  13. Image:3dpl 3dqv acr morph.pdb (632 bytes)
    2: ...th model) without the need for special alignment. Morph done by Eric Martz at the request of Raymond J. D...
  14. Image:Morph 2ipy-2b3x.pdb.gz (96 bytes)
    2: 20 image morph between 2ipy and 2b3x, from Yale server
  15. Image:3dqv trimer1 trimer2 morph.pdb.gz (153 bytes)
    2: Morph (Yale Morph Server beta.cgi, ID b318728-3599) between the two...
  16. Image:2oau 2vv5 morph.pdb.gz (93 bytes)
    2: Yale morph server (beta) morph from 2oau to 2vv5.
  17. Image:2oau 2vv5 morph cao.pdb.gz (228 bytes)
    2: ...ID=b182826-5521, the Yale Morph Server (beta.cgi) morphing 2oau to 2vv5. Only the alpha carbon atoms are ...
  18. Image:2oau 2vv5 27-112 morph.pdb.gz (284 bytes)
    2: ...in for the morph. http://www.molmovdb.org/cgi-bin/morph.cgi?ID=b286401-18956
  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)
    1: ...oerpositions and to create morph, see [[Jmol/Storymorph]].
    97: ...s a trimer with chains A, B, and C. Each chain is morphed individually
    113: // To save this step in the morph, un-comment the following three lines while runni...
    114: // fname = "morph" + i + ".pdb"
    118: ...es in preparation of calculating next step in the morph
  2. Image:3hg2to3.pdb.gz (19 bytes)
    1: morph 3hg2 to 3hg 3
  3. Image:Better3hg2to3.pdb.gz (18 bytes)
    1: 3hg2 to 3hg3 morph
  4. Art:Spike protein conformation change (371 bytes)
    3: Morph between 6xr8 and 6xra, animated to move like swim...
  5. Teaching Scenes, Tutorials, and Educators' Pages (12,171 bytes)
    66: *[[Lac repressor]]: Introduction, structure, morph of the conversion from non-specific to specific D...
    103: ...erin, a calcium-activated myristoyl switch]] with morph animations.
    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>
  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....
    136: ...with [[RMSD]] 2.4 &Aring;. The FATCAT-generated [[morph]] between the two models shows their similarity. ...
    140: [[Morph]] Between Models
  7. User:Alexander Grayzel/Sandbox 1 (15,974 bytes)
    46: ... On top of this, glycerol also has the ability to morph its diffusion pores to prevent water from enterin...
  8. Sculpting protein conformations (6,480 bytes)
    3: ...morphs]] in Proteopedia. Slides explaining how to morph a sculpted protein are available at [http://tinyu...
  9. Sandbox UC 9 (2,556 bytes)
    1: <Structure load='Insert PDB code or filename here' size='350' frame='true' al...
    13: ...a lipase ([[1trh]], [[1lpm]]).' scene='Lipase_lid_morph/Lightseagreen_hinge/1' />
    14: ...ase see the article [[Lipase]]. This ''Lipase lid morph'' article is a supplement to the main article on ...
    18: ...green'><b>LID</b></font> (<scene name='Lipase_lid_morph/Lightseagreen_hinge/1'>restore initial scene</sce...
    19: *<scene name='Lipase_lid_morph/Lightseagreen_hinge/4'>Open</scene> <font color='...
  10. Proteopedia:Practical Guide to Advanced Proteopedia Authoring and Its Use in Teaching (16,838 bytes)
    20: ...as those involved in ligand binding; see [[Morphs#Morphing Methods]].
  11. Image:3hg3to4.pdb.gz (87 bytes)
    1: morph of 3hg3 to 3hg4
  12. AlphaFold2 examples from CASP 14 (26,979 bytes)
    20: ...nerated by the [[Morphs#Linear_Morph_Server|Theis Morph Server]] by linear interpolation.</ref>. The only...
    23: ...lmovdb.org/wiki/info/index.php/Morph2_Server Yale Morph2 Server]. Homogenization method: homology modelin...
    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)
    39: ...roteopedia.org/wiki/scripts/Morphs/1osl_19_1l1m_9_morph/2.spt
    108: *[[Flaps Morph for HIV Protease]]
    112: *[[Lipase lid morph]]
    114: ...ensitive channels: opening and closing]] included MORPHS
  14. Eric Martz's Favorites (2,342 bytes)
    3: ...zyme to disc membranes in rod cells in the eye. [[Morphs]] of this transition are [[Recoverin, a calcium-...
    5: ...n 2004 ([[1osl]]) made possible a [[Lac repressor|morph of the DNA bending during specific recognition by...
    10: ...aminidase, Tamiflu and Relenza]] which includes a morph of the induced fit, and visualization of the cavi...
    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: ...rk into PDB when returning a morph from the pymol morph server
    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...
    73: ...[Flaps Morph for HIV Protease|HIV Protease: Flaps Morph]]
    82: *[[Lipase lid morph]]
  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)
    1: ...Channels/Cartoon/2' caption='Linear interpolation morph from [[3bkd]] to model 1 of [[2rlf]]. '>
    7: ...zed by rimantadine. (Neither drug is shown in the morph at right.)
    10: caption='Linear interpolation morph from [http://proteopedia.org/wiki/index.php/3bkd ...
    12: At right is a [[Morphs|linear-interpolation morph]] between 3BKD and 2RLF, showing the proposed ope...
    17: ...ue to the [[Morphs|linear interpolation method of morphing]].) Here are His and Trp <scene name='Proton_C...
  20. Image:Tres EH eMorph.pdb (57 bytes)
    1: A morph for testing the morphing features of Proteopedia.

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