1 Introduction STARTING a SPDB view Session Basic SPDB view Commands Advanced SPDB view Commands Ending a SPDB view Session 2 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 Introduction 3 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 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 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 A recorded video of these commandsvideo these commands Basic SPDB view Commands b. Using the menus 21 II. Using the Control Panel Using the Layers Infos Window Basic SPDB view Commands 22 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 24 25 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 27 28 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 30 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 32 33 34 Computing molecular surfaces 35 36 Computing electrostatic potential maps 37 38 39 Computing pseudo energy: mean force potential 40 41 42 Computing energy minimization 43 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 SwissModel>Submit Modeling 46 SwissModel>Submit Modeling count. Ending a DeepView Session I. Saving Data II. Closing DeepView 47 Any question???? 48 Superposing and calculation of Root Mean Squared deviation (RMSD) RMSD = 50 51 52