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2.  Introduction  STARTING a SPDB view Session  Basic SPDB view Commands  Advanced SPDB view Commands  Ending a SPDB view Session 2

3. Swiss-PdbViewer has been developped since 1994 by Nicolas Guex. Swiss-PdbViewer is tightly linked to SWISS-MODEL, (from SIB) Swiss-PdbViewer has many applications such as:  thread a protein primary sequence onto a 3D template,  can read electron density maps,  various modeling tools are integrated,  residues can be mutated,  And … http://spdbv.vital-it.ch/ Introduction 3

4. I. Loading Files II. Displaying Windows III. Obtaining Help Toolbar Layer name and window size (pixels) Graphic window Control panel STARTING a SPDB view 4

5. Basic SPDB view Commands I. Using the Toolbar a. Using the tools b. Using the menus Menus Tools click it to obtain help on the Toolbar PDB file icon Tools for basic functions Tools for advanced functions. 5

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20. 20 A recorded video of these commandsvideo these commands

21. Basic SPDB view Commands b. Using the menus 21

22. II. Using the Control Panel Using the Layers Infos Window Basic SPDB view Commands 22

23. Advanced SPDB view Commands I.Working on a Layer b. Searching commands Searching a molecule for a sequence pattern Searching a molecule for all patterns in the PROSITE database Searching SWISS-PROT and ExPDB databases 23

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26. Searching a molecule for a sequence pattern Searching a molecule for all patterns in the PROSITE database Searching SWISS-PROT and ExPDB databases Advanced SPDB view Commands 26

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29. Searching a molecule for a sequence pattern Searching a molecule for all patterns in the PROSITE database Searching SWISS-PROT and ExPDB databases Advanced SPDB view Commands 29

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31. Advanced SPDB view Commands I.Working on a Layer c. Computing commands Computing H-bonds Computing molecular surfaces Computing electrostatic potential maps Computing pseudo energy: mean force potential Computing energy: force field Computing energy minimisation 31

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34. 34 Computing molecular surfaces

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36. 36 Computing electrostatic potential maps

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39. 39 Computing pseudo energy: mean force potential

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42. 42 Computing energy minimization

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44. Homology Modeling Loading files Edit>BLAST Selection vs. ExPDB Fit>Magic Fit Alignment window SwissModel>Submit Modeling how to perform a submission to Swiss-Model in the Optimise (Project) mode

45. SwissModel>Submit Modeling http://swissmodel.expasy.org/

46. 46 SwissModel>Submit Modeling count.

47. Ending a DeepView Session I. Saving Data II. Closing DeepView 47

48. Any question???? 48

49. Superposing and calculation of Root Mean Squared deviation (RMSD) RMSD =

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