TOOLKIT

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

• Checklist

• Manaul

Sign-up sheets

• Microfluidizer

• Shaker

• Conference Room

Lab ordering website

Minus 80 Stock

NMR
• 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
• YOU MUST READ THIS BEFORE USING THE FPLC!!!!!
• 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
• 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
• CYANA
   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.