UMass Amherst

Welcome to the home page of BMB 695a,
Methods in Macromolecular Crystallography (Spring 2007)!

The UMass protein crystallography home page has moved to xtal.biochem.umass.edu

This journal club is organized by Scott Garman, Jeanne Hardy, and Karsten Theis.We share a common interest in structural biology, including X-ray crystallographic techniques. Our labs are all located on the 10th floor of Lederle Tower, along with the X-ray diffraction facility.

If you are looking for the home page of the UMass X-ray diffraction facility, you can find it here.

If you are looking for Karsten Theis' home page, it is here, while Scott Garman's home page is here, and Jeanne Hardy's is here.

Pictures of the UMass Macromolecular X-ray Diffraction facility open house are here.

Spring 2007 Journal Club Schedule (Biochem 695a, Methods in Macromolecular Crystallography):

Journal Club meets Fridays at 8:45 in 1030 LGRT. Participants can pick a paper on their own or talk to Jeanne, Karsten or Scott. Download files by following the links below.

Date
Topic
Presenter
Readings and Links
9 Feb 07
Making sense of Table 1
Khadine Higgins
Rhodes Chapter 8;
Kleywegt Model building (for reference)
16 Feb 07
Making sense of Table 1
(pt 2)
Abby Guce
Same as above, plus
Khadine and Abby's Powerpoint
23 Feb 07
Pattersons
Cassidy Dobson
Brenner page at Dartmouth;
Cassidy's powerpoint
2 Mar 07
Real Data for Pattersons
Round Table Discussion
Work the exercises in the Brenner page above;
Garman Pattersons.pdf
9 Mar 07
Solving Pattersons
Round Table Discussion
C2 space group handout; Garman Pattersons pdf
16 Mar 07
Pattersons and phases
Round Table Discussion
C2 space group handout; Garman Pattersons pdf
23 Mar 07
No meeting: Spring Break
30 Mar 07
More Solving Pattersons
Round Table Discussion
Karsten's slides from the x-ray minicourse:
1, 2, 3, 4;
Scott's Fourier handout in class
6 Apr 07
The Phase Problem
Round Table Discussion
Taylor 2003 (Note: 12MB!)
Homework questions

Group 1: Khadine, Cassidy, Witold
Group 2: Sravanti, Kristen P, Nivas
Group 3: Mike, Fabian, Will
13 Apr 07
Table 1 revisited
Round Table Discussion
Look at maps:
1. From Au phases (au.map)
2. From Pt phases (pt.map)
3. From Au + Pt phases (au_pt.map);
Garman_1998.pdf
20 Apr 07
Building into maps
Round Table Discussion
Practice model building:
3 Ang dm map (ccp4 format, 3MB)
2.4 Ang final map (ccp4 format, 8MB)
27 Apr 07
Discuss Building into maps
Work Session
Build a strand-turn-strand before coming to class:
Instructions: Interpretation of density pdf;
Starting coordinates: build.pdb;
Experimental map: 3 Ang dm map;
O bones data file: bones15rms.odb;
Kristen's notes on getting started with O: (.doc);
Mike's notes on making bones files: (.doc)
4 May 07
Finish up building
Work Session
Extend the trace from where we left off: b2.pdb
11 May 07
Molecular Replacement
Round Table Discussion
Before coming to class, try MR:
Model: 1F2Q.pdb
Reflections: mip3_f.mtz.zip
Help sheet: Garman_MR.pdf

 

 

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Biochem 695a (Macromolecular Methods Journal Club) from Spring semester 2005

Biochem 695a (Macromolecular Methods Journal Club) from Spring semester 2006