Biochem 660 - 2008 PyMol&1&39 L01: Desktop Molecular Graphics PyMol 1 From the preface of the User’s guide: “PyMOL was created in an efficient but highly pragmatic manner, with heavy emphasis on delivering powerful features to end users. Expediency has almost always taken precedence over elegance, and adherence to established software development practices is inconsistent. PyMOL is about getting the job done now, as fast as possible, by whatever means were available.” PyMol is a multiplatform molecular graphics software with many advanced features such as rendered cartoon ribbons and surfaces, internal ray tracing and movie tools and is fast becoming the new “standard” in molecular graphics. The PyMol web site is located at http://pymol.sourceforge.net/ Biochemistry students can download the latest PyMol version from a campus network at http://www.biochem.wisc.edu/it/resources.aspx Note: within the exercises, Bold text shows what actions are taken by the user : typing text or clicking the mouse. Whenever possible a “call for action” icon (√ or ✔) will be shown. - e - 1 PyMol&‐ & Exercise&A:&Download&a&PDB&from&the&repository & Reminder: Structures have a PDB ID code made of 4 letters and numbers. PDB files contain coordinates pertinent to the crystallographic arrangement of the molecules within the crystal. The biological functional entity can be either a multimer of the deposited structure, or just one of multiple copies within the file. In the following example we will download one functional biological subunit, in this case a monomer. ✔ TASK • Open a web browser such as Safari or Firefox. • Point your web browser to www.rcsb.org • In the Search box enter the following ID: 2biw and click SEARCH button40 PyMol&‐&1& • On the left column click Download Files to show submenus • Click the first option Biological UnitCoordinates 2 Note: DO NOT USE Biological Unit Coordinates 1 • The file is saved on the desktop as 2BIW.pdb2 Note: The file might be delivered as a gunzipped (.gz) file. However the browser should decode it automatically. You can now close your browser, or hide it (Command-H). Optional exercise: explore the text content of the PDB file 2BIW.pdb2 You can review details on the PDB file format in the previous section titled “Desktop molecular graphics: background essentials” and online at http://www.rcsb.org (On the left menu table click on “Dictionaries & File Formats” and select “PDB format.” In summary, PDB files are the simplest plain text files organized in column format in lines of at most 80 characters. Each line (record) starts with a keyword. The top of the file (header) contains informative records, while ATOM and HETATM records represent the 3D coordinates. Open 2BIW.pdb2 with a simple word processor (the simpler the better! For example “TextEdit on a Macintosh or “Wordpad” in Windows. Windows simple “Notepad” usually does not work because it does not translate end-of-line characters. Scroll up and down the text file and observe the contents. Since we only saved a portion of the original PDB data by selecting a biological unit monomer, the header is somewhat shorter (428 lines before the first ATOM record) than if we had saved the complete PDB file (998 lines; you can download the complete 2BIW.pdb file if you wish.) Note that within the 2BIW.pdb2 header, the XXXX next to the release date on the first line are replacing the 2BIW PDB ID code as 2BIW.pdb2 does not represent the complete PDB records.Biochem 660 - 2008 PyMol&1&41 H E A D E R 3 D - D A T A E N D HEADER OXIDOREDUCTASE 19-JAN-05 XXXX TITLE CRYSTAL STRUCTURE OF APOCAROTENOID CLEAVAGE OXYGENASE FROM TITLE 2 SYNECHOCYSTIS, NATIVE ENZYME COMPND APOCAROTENOID-CLEAVING OXYGENASE KEYWDS OXYGENASE,NON-HEME IRON,CAROTENOID CLEAVAGE,RETINAL KEYWDS 2 FORMATION, OXIDOREDUCTASE, DIOXYGENASE EXPDTA X-RAY DIFFRACTION AUTHOR D.P.KLOER, S.RUCH, S.AL-BABILI, P.BEYER, G.E.SCHULZ JRNL AUTH D.P.KLOER, S.RUCH, S.AL-BABILI, P.BEYER, G.E.SCHULZ JRNL TITL THE STRUCTURE OF A RETINAL-FORMING CAROTENOID JRNL TITL 2 OXYGENASE JRNL REF SCIENCE V. 308 267 2005 JRNL REFN ASTM SCIEAS US ISSN 0036-8075 REMARK 1 SEQRES 1 A 490 MET VAL THR SER PRO PRO THR SER SER PRO SER GLN ARG SEQRES 2 A 490 SER TYR SER PRO GLN ASP TRP LEU ARG GLY TYR GLN SER [. . . . . . . . . . . . ] MTRIX2 3 -0.756169 0.514705 -0.404088 13.98510 1 MTRIX3 3 0.610627 0.777006 -0.152957 118.86930 1 ATOM 1 N GLN B 12 16.794 -17.939 28.900 1.00 71.25 N ATOM 2 CA GLN B 12 16.091 -17.967 30.218 1.00 71.00 C ATOM 3 C GLN B 12 16.877 -17.181 31.273 1.00 69.76 C [. . . . . . . . . . . . ] ATOM 3766 CG2 THR B 490 47.002 -0.207 59.451 1.00 73.42 C ATOM 3767 O'' THR B 490 48.633 0.228 56.341 1.00 73.10 O TER 3768 THR B 490 HETATM 3769 FE FE B1492 30.259 6.403 38.822 1.00 45.64 FE HETATM 3770 O1 3ON B1491 26.391 21.062 36.210 1.00100.47 O HETATM 3771 C5 3ON B1491 25.099 20.591 36.637 1.00100.23 C [. . . . . . . . . . . . ] CONECT 3799 3798 CONECT 3800 3798 3801 CONECT 3801 3800 MASTER 0 0 0 36 154 0 24 1515742 4 37 152 END - e - 2 PyMol&‐ & Exercise&B:&Open&PyMol&and&load&PDB&file& PyMol or MacPyMol should be located within Applications > Classes on the DMC computer. Your instructor may give you a different location if necessary. ✔ TASK • double-click on the