Protein-RNA interactions of1 3 21.04.2017 Vizualization of structures by PyMol Disclaimer: any structure is just a model! ______________________________________________________________________ Get the pdb: pdb.org or pdbe.org Documentation about pdb file format: http://www.wwpdb.org/documentation/file-format Example: - go to pdb.org -> type in search ‘Nrd1’-> download entries 2LO6 and 3CLJ - open with text reader ______________________________________________________________________ Download Pymol: http://www.pymol.org/ Manuals and hints: http://pymolwiki.org or type help ______________________________________________________________________ To load pdb-file: • open Pymol -> File -> Open or • type fetch PDBID Save pymol session: • Pymol -> File -> Save session as … or • save folder/folder/…/thisSession.pse To save logs for the session and use later as a script: • File -> Log or log_open log1.pml ______________________________________________________________________ To see sequence: • button S in the right bottom corner or • type set seq_view, 1 Pymol panels: A - action S - show H - hide L - label C - color Protein-RNA interactions of2 3 21.04.2017 Vizualization modes: lines (e.g. show lines) sticks cartoon (use dss, dss defines secondary structure based on backbone geometry and hydrogen bonding patterns) ribbon surfase spheres Color: by element by secondary structure by chain Selection: http://pymol.sourceforge.net/newman/user/S0220commands.html select name, (selection) atom type: name or n., select carbons, name ca+cb+cg+cd residue type: resn or r., select aas, resn asp+glu+asn+gln ; select bases, resn a+g residue number: resi or i., select nterm, resi 1-10 chain: chain or c., select firstch, chain a ______________________________________________________________________ NMR structures (try on 2LO6): • to see the whole bundle set all_states, on • to align states intra_fit PDBID • to split all states as separate objects split_states PDBID • hide hydrogens hide (hydro)/show (hydro) ______________________________________________________________________ X-ray structures (try on 3CLJ, 2GQW) Lamb, A.L., Kappock, T.J., and Silvaggi, N.R. (2015). You are lost without a map: Navigating the sea of protein structures. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1854, 258–268. • color by chain • split chains: split_chains • hide water hide (solvent) • add hydrogens: action -> hydrogen -> add • select water select water, resn hoh • color by B-factor: spectrum b, blue_white_red, minimum=20, maximum=50 as cartoon cartoon putty • generation of symmetry and electron density maps (http:// pymol.sourceforge.net/newman/user/S0400xtal.html) ______________________________________________________________________ Protein-RNA interactions of3 3 21.04.2017 Electrostatics (to see positive, negative, neutral areas) Action -> generate -> vacuum electrostatics -> protein contact potential Distance measurements Wizard -> measurement distance test, 10/CA, 50/CA select around10, i. 12 a. 10 Hydrogen-bonds: http://www.protein.osaka-u.ac.jp/rcsfp/supracryst/suzuki/jpxtal/ Katsutani/en/hydrogenbond.php Action -> find-> polar contacts -> select from menu Get surface : http://www.pymolwiki.org/index.php/Get_Area 1. select area of interest -> Action -> duplicate 2. Action -> compute -> select from menu Alignment 1. Load structures of interest 2. Action -> align -> to molecule several alternatives: http://pymolwiki.org/index.php/ Cealign#Multiple_Structure_Alignments Interface residues: http://www.pymolwiki.org/index.php/InterfaceResidues ______________________________________________________________________ Vizualization for publication: http://www.pymolwiki.org/index.php/ Publication_Quality_Images bg_color white ray 1000, 1000 save test_image.png ______________________________________________________________________ Scripting: http://pymolwiki.org/index.php/Simple_Scripting ______________________________________________________________________ Multiple sequence alignment visualisation: ConSurf server http://consurf.tau.ac.il/ LigPlot: Automatically generates schematic diagrams of protein-ligand interactions for a given PDB file. http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/ UCSF Chimera - more sophisticated then PyMol : https://www.cgl.ucsf.edu/chimera/