UW-Madison BIOCHEM 660 - Desktop Molecular Graphics PyMol 1 (42 pages)

Previewing pages 1, 2, 3, 20, 21, 40, 41, 42 of 42 page document View the full content.
View Full Document

Desktop Molecular Graphics PyMol 1



Previewing pages 1, 2, 3, 20, 21, 40, 41, 42 of actual document.

View the full content.
View Full Document
View Full Document

Desktop Molecular Graphics PyMol 1

61 views


Pages:
42
School:
University of Wisconsin, Madison
Course:
Biochem 660 - Biochemical Techniques
Unformatted text preview:

Biochem 660 2008 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 button PyMol 1 39 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 40 PyMol 1 Biochem 660 2008 HEADER TITLE TITLE COMPND KEYWDS KEYWDS EXPDTA AUTHOR JRNL JRNL JRNL JRNL JRNL REMARK SEQRES SEQRES MTRIX2 MTRIX3 ATOM ATOM ATOM ATOM ATOM TER HETATM HETATM HETATM CONECT CONECT CONECT MASTER END H E A D E R 3 D D A T A E N D OXIDOREDUCTASE 19 JAN 05 XXXX CRYSTAL STRUCTURE OF APOCAROTENOID CLEAVAGE OXYGENASE FROM 2 SYNECHOCYSTIS NATIVE ENZYME APOCAROTENOID CLEAVING OXYGENASE OXYGENASE NON HEME IRON CAROTENOID CLEAVAGE RETINAL 2 FORMATION OXIDOREDUCTASE DIOXYGENASE X RAY DIFFRACTION D P KLOER S RUCH S AL BABILI P BEYER G E SCHULZ AUTH D P KLOER S RUCH S AL BABILI P BEYER G E SCHULZ TITL THE STRUCTURE OF A RETINAL FORMING CAROTENOID TITL 2 OXYGENASE REF SCIENCE V 308 267 2005 REFN ASTM SCIEAS US ISSN 0036 8075 1 1 A 490 MET VAL THR SER PRO PRO THR SER SER PRO SER GLN ARG 2 A 490 SER TYR SER PRO GLN ASP TRP LEU ARG GLY TYR GLN SER 3 0 756169 0 514705 0 404088 13 98510 1 3 0 610627 0 777006 0 152957 118 86930 1 1 N GLN B 12 16 794 17 939 28 900 1 00 71 25 2 CA GLN B 12 16 091 17 967 30 218 1 00 71 00 3 C GLN B 12 16 877 17 181 31 273 1 00 69 76 3766 CG2 THR B 490 47 002 0 207 59 451 1 00 73 42 3767 O THR B 490 48 633 0 228 56 341 1 00 73 10 3768 THR B 490 3769 FE FE B1492 30 259 6 403 38 822 1 00 45 64 3770 O1 3ON B1491 26 391 21 062 36 210 1 00100 47 3771 C5 3ON B1491 25 099 20 591 36 637 1 00100 23 3799 3798 3800 3798 3801 3801 3800 0 0 0 36 154 0 24 1515742 4 37 152 N C C C O FE O C 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 PyMol icon to launch the software Note Some versions of PyMol have the top and bottom panels in separate windows but offer the same interface Type the next commands after PyMOL within the top line command PyMol 1 41 TASK PyMOL cd desktop Note the echo on the text area above PyMOL pwd this will echo Users DMC Desktop or a similar path On a Windows system the path would begin with C Note PyMol uses many Unix commands cd change directory pwd present working directory PyMOL load 2BIW pdb2 This will load the structure and echo information in the text panel as reproduced to the right Note file name is case sensitive PyMOL load 2BIW pdb2 HEADER OXIDOREDUCTASE 19 JAN 05 XXXX TITLE CRYSTAL STRUCTURE OF APOCAROTENOID CLEAVAGE OXYGENASE FROM TITLE 2 SYNECHOCYSTIS NATIVE ENZYME COMPND APOCAROTENOID CLEAVING OXYGENASE ObjectMolecule Read secondary structure assignments ObjectMolecule Read crystal symmetry information Symmetry Found 4 symmetry operators CmdLoad 2BIW pdb2 loaded as 2BIW pdb2 Note XXXX substituted for 2BIW within the saved PDB text because we opted to select only a portion of the original PDB data when we chose to use a biological subunit rather than the complete entry The XXXX reflects that this is a partial or altered PDB file Note why not use the File Open menu sequence Good question You can actually try that option and it might work on your current system However you will likely find that when you get to the Open entry of the …


View Full Document

Access the best Study Guides, Lecture Notes and Practice Exams

Loading Unlocking...
Login

Join to view Desktop Molecular Graphics PyMol 1 and access 3M+ class-specific study document.

or
We will never post anything without your permission.
Don't have an account?
Sign Up

Join to view Desktop Molecular Graphics PyMol 1 and access 3M+ class-specific study document.

or

By creating an account you agree to our Privacy Policy and Terms Of Use

Already a member?