Web Resources:
A review of crystallography from Lawrence Livermore National Lab.

A course on reflections from crystal planes.

A review of Fourier Transforms.

An excellent tutorial on structure factors can be found in the UK.

A tutorial illustrating diffraction, including reciprocal lattices and the Ewald called XRay-view.

Yet another tutorial on X-Ray & Neutron Diffraction.

Study Guides:

Study Guide 1

Study Guide 2

Study Guide 3

Study Guide 4

Study Guide 5

Study Guide 6
 

These on-line additions to your study guides will rely on the use of several types of tools. This first is a browser based tool for a quick first-look at the structures called Chime. The next type of tool is a molecular structure program. The software that will be most heavily relied upon is a program called Swiss-PDB. This is a free program that (in my opinion) out-competes the most expensive packages. If you would like to try other packages, I can recommend Grasp, Rasmol, Insight, or Mol Mol. Some will run on other platforms (such as Unix) if you do not have access to a Mac or a PC on which to run Swiss-PDB.


















Study Guide1:
Doyle et al.,Science, 3 April 1998


Color Images:
  • Figure 2
  • Figure 3
  • Figure 4
  • Figure 5
  • Figure 6
  • Figure 7
  • Figure 8
    		•  For a Chime overview : Click here.

     Download Swiss-PDB'd protein : Click here.

     Download the raw coordinates : Click here. 

    NOTE: To download coordinates (not the Chime overview) you need to click and hold the button down until you get a menu. At the menu select Save this link as...

    Chang et al.,Science, 18 December 1998

    Color Images:
  • Figure 2
  • Figure 4
  • Figure 5
  • Figure 6
      •  
    		 For a Chime overview : Click here.

     Download Swiss-PDB'd protein : Click here.

     Download the raw coordinates : Click here. 

    NOTE: To download coordinates (not the Chime overview) you need to click and hold the button down until you get a menu. At the menu select Save this link as...

    Study Guide 2:

    MacKinnon et al., Science, 18 December 1998

    Color Images:
  • Figure 3c
  • Figure 4
    		•  For a Chime overview : Click here.

     Download Swiss-PDB'd protein : Click here.

     Download the raw coordinates : Click here. 

    NOTE: To download coordinates (not the Chime overview) you need to click and hold the button down until you get a menu. At the menu select Save this link as...


    Huber et al., JMB, 5 February 1992
    Lecture Transparencies:
  • Overview
  • Helix Capping
  • 3 Features
  • Neat Features

    •  

     
     
     
     
     
     
     
     
     
     
     
     
     
     
     

    Gating Reference:

    Liemann et al., J. Molecular Biology, 1996, vol. 258, p.555-561. 

    		 For a Chime overview : Click here.

     Download Swiss-PDB'd protein : Click here.

     Download the raw coordinates : Click here. 

    NOTE: To download coordinates (not the Chime overview) you need to click and hold the button down until you get a menu. At the menu select Save this link as...

    Weiss et al., JMB, 20 September 1992
    Lecture Transparencies:
  • Agitoxin and Porin
    		•  For a Chime overview : Click here.

     Download Swiss-PDB'd protein : Click here.

     Download the raw coordinates : Click here. 

    NOTE: To download coordinates (not the Chime overview) you need to click and hold the button down until you get a menu. At the menu select Save this link as...

    Study Guide 3:
     

    Wang et al., Nat.Struct.Bio., June 1998
    Color Images:
  • Figure 3c
  • Figure 5
  • Figure 6

    •  

     
     
     
     
     
     
     
     
     
     
     

    Lecture Transparencies:

  • Overview
  • Acidic Residues
  • Hydrophobics
  • SAH and DBH
    		•  For a Chime overview : Click here.

     Download Swiss-PDB'd protein : Click here.

     Download the raw coordinates : Click here. 

    NOTE: To download coordinates (not the Chime overview) you need to click and hold the button down until you get a menu. At the menu select Save this link as...


    Chattopadhyaya et al., JMB, 20 December 1992-Calmodulin Structure

     

    Lecture Transparencies:

  • Overview of 3 Structures

    •      		 For a Chime overview : Click here.

     Download Swiss-PDB'd protein : Click here.

     Download the raw coordinates : Click here. 

    NOTE: To download coordinates (not the Chime overview) you need to click and hold the button down until you get a menu. At the menu select Save this link as...

    Meador et al., Science, 28 August 1992 1-Calmodulin Peptide Complex

     

    Lecture Transparencies:

  • Peptide Binding

    •      		 For a Chime overview : Click here.

     Download Swiss-PDB'd protein : Click here.

     Download the raw coordinates : Click here. 

    NOTE: To download coordinates (not the Chime overview) you need to click and hold the button down until you get a menu. At the menu select Save this link as...

    Cook, Biochem., 27 December 1994-Calmodulin TFP Complex

     

    Lecture Transparencies:

  • Overview of Binding
  • Detail of Inhibition

    •      		 For a Chime overview : Click here.

     Download Swiss-PDB'd protein : Click here.

     Download the raw coordinates : Click here. 

    NOTE: To download coordinates (not the Chime overview) you need to click and hold the button down until you get a menu. At the menu select Save this link as...

    Study Guide 4:
     

    Armstrong et al., Nature, 29 October1998-Glutamate Receptor

     

    Color Images:

  • Figure 2
  • Figure 3
  • Figure 4a
  • Figure 4b/c

    •  

     
     
     
     
     
     
     

    Lecture Transparencies:

  • Overview of iGluR
  • Kainate Binding

    •      		 For a Chime overview : Click here.

     Download Swiss-PDB'd protein : Click here.

     Download the raw coordinates : Click here.

    NOTE: To download coordinates (not the Chime overview) you need to click and hold the button down until you get a menu. At the menu select Save this link as...


    Sun et al., JMB, 1998-Glutamine Binding Protein (Closed)

     

    Lecture Transparencies:

  • Alignment w/Open Form
  • Alignment w/iGluR

    •      		 For a Chime overview : Click here.

     Download Swiss-PDB'd protein : Click here.

     Download the raw coordinates : Click here. 

    NOTE: To download coordinates (not the Chime overview) you need to click and hold the button down until you get a menu. At the menu select Save this link as...

    Hsiao et al., JMB, 1996-Glutamine Binding Protein (Open)

     

    Lecture Transparencies:

  • Alignment w/iGluR

    •      		 For a Chime overview : Click here.

     Download Swiss-PDB'd protein : Click here.

     Download the raw coordinates : Click here. 

    NOTE: To download coordinates (not the Chime overview) you need to click and hold the button down until you get a menu. At the menu select Save this link as...

    Home-Built AMPA

     

    Lecture Transparencies:

  • CPK Representations
  • AMPA docked into iGluR

    • NOTE: this is not the final docking    		 For a Chime overview : Click here.

     Download Swiss-PDB'd protein : Click here.

     Download the raw coordinates : Click here. 

    NOTE: To download coordinates (not the Chime overview) you need to click and hold the button down until you get a menu. At the menu select Save this link as...

    Pflugrath et al., JMB, 1988-Sulfate Binding Protein

     

    Lecture Transparencies:

  • Helix Dipoles

    •      		 For a Chime overview : Click here.

     Download Swiss-PDB'd protein : Click here.

     Download the raw coordinates : Click here. 

    NOTE: To download coordinates (not the Chime overview) you need to click and hold the button down until you get a menu. At the menu select Save this link as...

    Study Guide 5:
     

    Nogales et al., Nature, 8 January 1998

     

    Color Images:

  • Figure 2
  • Figure 3
  • Figure 4a
  • Figure 4b/c

    •  

     
     
     
     
     
     
     

    Lecture Transparencies:

  • Microtubule Model
  • Overview
  • Rossmann Fold
  • Nucleotide Binding
  • Taxol Binding
  • Binding Sites

    •      		 For the Dimer Building:
    Download Swiss-PDB'd structure of a-tubulin: Click here.
    Download Swiss-PDB'd structure of b-tubulin: Click here.

    The Usual Stuff:
    For a Chime overview : Click here.

     Download Swiss-PDB'd protein : Click here.

     Download the raw coordinates : Click here. 

    NOTE: To download coordinates (not the Chime overview) you need to click and hold the button down until you get a menu. At the menu select Save this link as...

    Study Guide 6:
     

    Kull et al., Nature, 11 April 1996

     

    Color Images:

  • Figure 1a
  • Figure 1b
  • Figure 2a/b
  • Figure 2c
  • Figure 3a
  • Figure 3b
  • Figure 3c

    •  

     
     
     
     
     
     
     

    Lecture Transparencies:

  • Overview
  • Nucleotide Binding Site
  • Tubulin Binding Site

    •      		 For a Chime overview : Click here.

     Download Swiss-PDB'd protein : Click here.

     Download the raw coordinates : Click here. 

    NOTE: To download coordinates (not the Chime overview) you need to click and hold the button down until you get a menu. At the menu select Save this link as...

    Sablin et al., Nature, 11 April 1996

     

    Color Images:

  • Figure 1a
  • Figure 1b
  • Figure 2a
  • Figure 2b/c
  • Figure 3

    •  

     
     
     
     
     
     
     

    Lecture Transparencies:

  • Overview
  • Dimer
  • Nucleotide Binding
  • Microtubule Binding
  • Neck Region

    •      		 For the Modeling:
    Download Swiss-PDB'd structure of Ncd monomer: Click here.

    The Usual Stuff:
    For a Chime overview : Click here.

     Download Swiss-PDB'd protein : Click here.

     Download the raw coordinates : Click here. 

    NOTE: To download coordinates (not the Chime overview) you need to click and hold the button down until you get a menu. At the menu select Save this link as...

    Sosa et al., Cell, 25 July 1997

    Color Images:

  • Figure 1
  • Figure 2
  • Figure 3
  • Figure 4

    • Rayment et al., Science, 1993

    Lecture Transparencies:

  • Overview
  • Nucleotide Binding Site
  • From Nucleotide to Converter
  • Ncd, Kinesin & Myosin Nucleotide Binding Site Alignements


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