Homology Modeling: Protocols and Concepts

Class Location: NCI-Library, NCI-Frederick, MD
Date: 04/17/2003

Exercise1: Getting familiarize with Swiss-PdbViewer.

1. Click open the Swiss-PdbViewer (Fig). Preferences >> Network Type in the File Server www.swissmodel.unibas.ch and for port 27000. Click here to see the picture. Note that the "Path of local PDB files" decides the directory where SwissPDBViewer decides to store the downloaded files. Go to Preferences >> Swiss-Model and make sure you have correct links for the modellin and template servers as http://swissmodel.expasy.org/cgi-bin/sm-submit-request.cgi and http://swissmodel.expasy.org/cgi-bin/blastexpdb.cgi. Also make sure you type in your name and an E-mail address in the respective boxes. Swiss-Model server will use the email address provided above to send the results from the modeling server. For this class, we are going to use email-accounts accessible via net-browsers (ex. hotmail etc.).
2. For help at any time, click the question mark looking symbol,
3. Also click on Preferences >> General... and UNCHECK "Show Log File Upon Loading" and the "Show Log file upon loading".
4. Click on File >> import... The Import radio opens up (Figure). Click and type 7lyz (PDB ID for lysozyme) on the Name window, and click on the button PDB file to download the pdb file from the server. The file will be downloaded to the directory already chosen in the the Preferences >> Network option, (Figure). Lysozyme will be displayed on the main screen (Figure).
5. Explore the group of buttons
6. Explore the second group of buttons
7. Use to view the contents of the PDB. One can do a lot of things with this view.
8. Go to Window >> Control Panel , to open the Control Panel module. Control Panel is an important module in the Swiss-PDBViewer. For more information, please refer to the user guide of Swiss-PDBviewer.
9. Open the Window >> Alignment and Window >> Layers Info & explore them.
10. Click on Select >> All (all atoms in the molecule) and go to Window >> Ramachandran Plot to see the Ramachandran map for 7lyz.
11. Click on Select >> None . Then open Window >> Control Panel . Scroll down to CYS94 , left-click on the CYS94 (under the group column) to select the residue. You will notice that the color of the residue name in the control panel will change to Red . Also click on the column under labl to add a check mark, you can also see on the main graphics window that a residue-label added to the CYS94 residue. Note that the font and its characteristics can be changed using the Preferences >>> Labels.... Now zoom in using so that you can see CYS94 clearly. Please use the following buttons, and to achieve the objective. Note to clear any User Lables, use Display >> Label Kind >> Clear User Labels you have added by using the option. Once you have zoomed in, hit the button and select (left-click) any atom in the residue 94 (CYS). As you select an atom, Display Radius button opens up (see figure) , check on the Select groups that are within and enter "7 Angstroms of the picked" and hit OK . By clicking OK, you have selected all the residues around 7 Angstroms of CYS 94. You can see the corresponding residue names change to red color in the Control Window . Click on the main window, and hit Enter button in your key-board to display only the selected residues. You can also use the button to zoom/center the view.
12. Finally, to display the secondary structure of 7lyz. Do the following: Go to Select >> All to select all the atoms and hit enter to display all the atoms. Go to control panel and left-click on the ribn to display the secondary structure of the selected atoms.

Contact Info: Dr. S. Ravichandran 
              Advanced Biomedical Computing Center, 
              NCI-Frederick, 
              Bldg 430, Frederick, MD 21702
              Tel:  301-846-1991 
              Email: sravi@ncifcrf.gov