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Wet Lab | Data Processing | PYMOL | Data Collection | NMRPipe Data Processing | Data analysis | Structure Calculation and Analysis

Lap Monitoring | HHMI VPN connections | IT related | Allegra X 30 manual | MASS Photometry


Gel Images


Guideline for deposition of NMR structures to the PDB




Sign-up sheets



Conference Room

Lab ordering website

Minus 80 Stock

Procedure to clean shaped NMR tubes
Which NMR tubes to use?
How to setup RNA exp on NMR by Jan
How to setup a methyTrosey exp on NMR by Jan

Wet Lab

Autoclave Protocol Checklist by Karndeep

Q5 NEB mutagenesis Protocols by Janae

pFIVORF2rep Maxipreps Protocols by Janae

Liposome extrusion Protocols by Janae
PF1 Phage Protocols by Canessa
(To provide feedback, please download this word version, and provide it to Canessa in track change mode)
Competent Cell Preparation
• Protein Expression
• NMR Sample Preparation
Standard Reagent Recipes for the HHMI lab at UMBC
• Instructions on how to prepare Phage to measure Dipolar Coupling Constants
T7 RNA Polymerase Preparation
TALON Metal Affinity Resin User Manual
HIV-NC Preparation, supplement
• MMLV-NC Preparation

FPLC Protocol for Undergraduates
FPLC Protocol for Graduates and Postdocs
AKTA FPLC system manual
AKTA FPLC, Making your first run
AKTA Prime manual
AKTA Prime: Cleaning and Maintenance Protocols
Minimal Media Cell Growth


Data Processing
Processing NMR NOESY data basic

•Processing for all NMR instruments


PyMOL Manual(updated 08/16/2011)
Dr. Summer's notes
Pymol Website


Data Collection
Protein NMR Book
How to setup TROSY experiment


NMRPipe Data Processing

Overview: Frank Delaglio's paper from J. Biomol. NMR
NIH Documentation: man pages, etc
NMRPipe conversion and processing scripts


Data Analysis
• NMRViewJ
• NMRViewJ Website

How to run miltiple NVJ seesions
How to setup strips display
How to do titration analysis

Structure Calculation and Analysis
   How to do protein structure calculations by Janae.

• ClustalW Guide : A multiple sequence alignment program for DNA or proteins.
   Can match up to 500 sequences.

• MidasPlus molecular viewer.
• Molmol (molecular viewer) command reference and tutorial. Can also be used to
   generate final figures.

• GRASP view PDB files and create surface maps (e.g. electrostatic surface potential).
• Rasmol a simple viewer for PDB files
• Procheck (Ramachandran plots, quality of structures)
• Locally developed programs
• AMBER (Assisted Model Building with Energy Refinement)
• How to Protonate crystal structures in AMBER ?

AVANTI J-E Centrifuge
Instructions and Manual for using the AVANTI J-E Centrifuge.