TOOLKIT
Wet Lab |
Data Processing | PYMOL | Data
Collection | NMRPipe Data Processing |
Data analysis | Structure
Calculation and Analysis | Figure Generation | How-to's | Molecular
Cloning | Epson 900n | XWINPLOT | Miscellaneous | Phage
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
AVANTI J-E Centrifuge
• Instructions and Manual for using the AVANTI J-E Centrifuge.
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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