Toolkit   Wet Lab  • Cloning  • 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  • YOU MUST READ THE FOLLOWING BEFORE USING THE FPLC!!!!!  • 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 for all NMR instruments   PYMOL  • Dr. Summer's notes  • Pymol Website Data Collection  • Pulse Sequences    • Bruker DMX 600    • Bruker DRX 800    • General Electric Omega 600  • GE Omega 600  • Bruker DMX 600 / DRX 800 NMRPipe Data Processing  • Overview: Frank Delaglio's paper from J. Biomol. NMR  • NIH Documentation: man pages, etc  • NMRPipe conversion and processing scripts Data Analysis  NMRView    • NMRView version 3: Original documentation that comes with nv3.    • NMRView version 3: HHMI scripts to do various things    • NMRView version 2.1: Original documentation that comes with nmrview 2.1. Use of nv3    • instead of version 2.1 is strongly encouraged    • NMRView version 4    • NMRView version 5    • NMRView Website    • Locally added nv3 scripts, etc. (/hhmi/nv3/hhmi)      • How to set up your account to use nv3      • nv3 startup script (/usr/groupS/bin/nv3)      • Things to put in startup file    • How to make plot files  • GE Omega 600 Structure Calculation and Analysis  • DYANA (pdf format): calculates structures of proteins/nucleic acids in torsion angle    space. Here is how to get Netscape to view a pdf file instead of downloading it to the disk.  • 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)  • Doing superpositions and RMSDs using Midas and some of the locally developed    programs  • Locally developed programs  • AMBER (Assisted Model Building with Energy Refinement)     • How to Protonate crystal structures in AMBER ? Figure Generation  • Molscript publication quality figure generation  • Raster3D rendering engine for molecular graphics. In our lab, input to raster3d is usually    from the output of a molscript or mscript run  • Mscript (wrapper around molscript/raster3d programs)  • Converting to various formats How-to's  • Raster3d to Illustrator  • Stereo Plots with molscript/molmol  • Getting Netscape to view a pdf file instead of downloading it to the disk  • Color Figures  • Black and White Figures Molecular Cloning  • Molecular Cloning Website  • Login Email address - cstove1@hhmi.umbc.edu  • Login Password - mchhmi Epson 900n  • Printing Postscript files on Epson 900n with PostShop software XWINPLOT  • Using xwinplot on xwinnmr Miscellaneous  • Non-SGI Unix programs (/usr/local/bin, /usr/local/src)  • Scientific programs (/usr/groupS/bin, /usr/groupS/src)  • Locally developed programs in alphabetical order (/usr/groupS/bin, /usr/groupS/src)  • Locally developed programs grouped by topic (/usr/groupS/bin, /usr/groupS/src)  • How to change window managers on the SGIs. Includes short sections on what a window   manager is and why you might want to switch. Phage  • Instructions on how to prepare Phage to measure Dipolar Coupling Constants.

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